iDARTS: individualized Deep-learning Analysis of RNA Transcript Splicing

Installation

Installation of the required packages can be easy by using Anaconda.

Install required packages

conda create -n idarts python=2.7  # optional
conda activate idarts              # optional
conda install -c bioconda viennarna==2.2.10
conda install tensorflow==1.9.0
conda install keras==2.2.4
conda install bedtools
conda install pysam
conda install pandas
conda install regex
conda install pyyaml
conda install pyBigWig
pip install scikit-image
conda install cyvcf2
pip install psutil
pip install joblib
pip install tqdm

Clone the repository and then download resource files

# clone the repository
git clone https://github.com/xinglab/iDARTS

# download resources
cd iDARTS
# change the permission of iDARTS (on Linux server)
chmod +x ./bin/iDARTS
./bin/iDARTS get_resources -o /path/to/directory/

Usage

iDARTS allows users to take a Variant Call Format (VCF) file containing variants of interests and make predictions on either pre-compiled (annotated) or user-provided AS events, based on iDARTS DNN trained on GTEx data and reference RBP expression levels across 53 GTEx tissues. The software output includes the predicted splicing levels (PSI values) of the reference and variants alleles, as well as the predicted variant effects on splicing (ΔPSI) in GTEx tissue types. iDARTS can also make predictions based on user-provided RBP expression levels for specific sample types of interest. When a VCF file is not provided, iDARTS reports predicted splicing levels (PSI values) for AS events of interest.

Predicting effects of variants on splicing

iDARTS is a robust and flexible computational framework for quantitative prediction of alternative splicing (AS) profiles. It can take several types of inputs.

Input:

Option 1. User-provided VCF file
- The pre-compiled AS events and RBP expression levels across 53 GTEx tissues will be used for prediction.
Option 2. User-provided VCF file and AS events
- The pre-compiled RBP expression levels across 53 GTEx tissues will be used for prediction.
- iDARTS can make predictions for SE, A3SS, and A5SS. The format of each AS type can be found in rmats-turbo. More specifically:
  - Shared columns:
    - ID: rMATS event id
    - GeneID: Gene id
    - geneSymbol: Gene name
    - chr: Chromosome
    - strand: Strand of the gene
  - SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
    - The inclusion form includes the target exon (exonStart_0base, exonEnd)
  - A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
    - The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
Option 3. User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest
- The preparation of AS events can be found in the above Option 2.
- iDARTS can make predictions for specific sample types of interest. This is enabled by preparing input gene expression file (TPM values quantified by Kallisto).
- The format of gene expression file:
  - Column Name
    - GeneID: Gene id
    - Sample1,Sample2,Sample3,...: Expression levels of different samples separated by comma

Output:

iDARTS outputs two result files with user-defined file name prefix:

No.	File Name	Description
1	`output_file_name_prefix`.vcf	The output VCF file contains information of each variant and its predicted ΔPSI with the maximum absolute value across all provided mapped splicing events in tissue or samples. (iDARTS will make predictions only if variants are within 300nt of target exons.)
2	`output_file_name_prefix`.iDARTS_prediction	The output iDARTS prediction file provides predicted splicing levels and ΔPSI across all tissues or samples for each variant in each splicing event as well as predicted splicing levels in each tissue or sample.

1. output_file_name_prefix.vcf

CHROM: Chromosome name
POS: Position
ID: SNP ID
REF: Reference allele
ALT: Alternative allele
QUAL: Not provided
FILTER: Not provided
INFO: iDARTS=AS type|Predicted ΔPSI.
- The predicted ΔPSI shows the maximum effect of the variant on splicing when considering all mapped AS events in samples.
- For SE events, if the predicted ΔPSI is positive, the variant causes higher inclusion for the target exon, and if the predicted ΔPSI is negative, the variant causes lower inclusion for the target exon.
- For A3SS/A5SS events, if the predicted ΔPSI is positive, the variant causes higher inclusion for the longer exon, and if the predicted ΔPSI is negative, the variant causes lower inclusion for the longer exon.

2. output_file_name_prefix.iDARTS_prediction

Shared columns:

SNP_ID: SNP ID of the variant
max_deltaPSI: The predicted ΔPSI with the maximum absolute value across all samples for each variant and AS event pair. This score can be used to investigate the effects of variants on specific splicing events.
Pos0base: The position of the variant (0-based)
Ref: Reference allele of the variant
Alt: Alternative allele of the variant
GeneID: Gene ID
geneSymbol: Gene name
chr: Chromosome name
strand: strand of the gene

AS event specific columns:

SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
- The inclusion form includes the target exon (exonStart_0base, exonEnd)
A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
- The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)

iDARTS Prediction columns: (Suppose we have three samples with sample name Sample1, Sample2, and Sample3 specified in user-provided RBP expression levels of sample types. When not provided, the RBP expression levels across 53 GTEx tissues will be used.)

Sample1_ref_PSI: The predicted reference PSI of the target AS event in Sample1
Sample2_ref_PSI: The predicted reference PSI of the target AS event in Sample2
Sample3_ref_PSI: The predicted reference PSI of the target AS event in Sample3
Sample1_deltaPSI: The predicted ΔPSI of the target AS event in Sample1
Sample2_deltaPSI: The predicted ΔPSI of the target AS event in Sample2
Sample3_deltaPSI: The predicted ΔPSI of the target AS event in Sample3

Example

Example 1:

Input: User-provided VCF file

VCF file needs to be sorted and have an index file that ends with .idx.
Example code:

bcftools sort ./example/example.vcf > ./example/example.sorted.vcf
bgzip ./example/example.sorted.vcf
tabix -p vcf ./example/example.sorted.vcf.gz

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -o ./example/example_iDARTS_pred

Example 2:

Input: User-provided VCF file and AS events

VCF file needs to be sorted (Please see Example 1 for more details).
The example of SE event can be found in ./example/example.SE_events.txt.

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -i ./example/example.SE_events.txt -o ./example/example_iDARTS_pred

Example 3:

Input: User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest

VCF file needs to be sorted (Please see Example 1 for more details).
The example of SE event can be found in ./example/example.SE_events.txt.
The example of RBP expression levels for different samples (here we take 53 tissues and cell types in GTEx as examples) can be found in ./example/example.RBP_expression_in_tissues.txt.

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events and RBP expression levels

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -i ./example/example.SE_events.txt -e ./example/example.RBP_expression_in_tissues.txt -o ./example/example_iDARTS_pred

Output (Example1, Example2, and Example3):

Example1, Example2, and Example3 have the same output.

./example/example_iDARTS_pred.vcf

##fileformat=VCFv4.2
##fileDate=20220907
##reference=GRCh37/hg19
##INFO=<ID=iDARTS,Number=.,Type=String,Description="iDARTS variant prediction. Maximum absolute deltaPSI across all tissues">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
2	110905531	2_110905531_C_T_b37	C	T	.	.	iDARTS=SE|-0.212
2	166854706	2_166854706_G_C_b37	G	C	.	.	iDARTS=SE|-0.2885
5	112102045	5_112102045_G_T_b37	G	T	.	.	iDARTS=SE|-0.4181
8	68066380	8_68066380_C_G_b37	C	G	.	.	iDARTS=SE|-0.1084
11	47369212	11_47369212_G_C_b37	G	C	.	.	iDARTS=SE|-0.3383
11	94219111	11_94219111_G_A_b37	G	A	.	.	iDARTS=SE|-0.3088
13	52535985	13_52535985_A_C_b37	A	C	.	.	iDARTS=SE|-0.0915
14	73637762	14_73637762_A_G_b37	A	G	.	.	iDARTS=SE|-0.2253
16	 2098764	  16_2098764_C_G_b37	C	G	.	.	iDARTS=SE|-0.1588
X	135112295	X_135112295_G_A_b37	G	A	.	.	iDARTS=SE|-0.2213

./example/example_iDARTS_pred.iDARTS_prediction

SNP_ID	max_deltaPSI	Pos0base	Ref	Alt	GeneID	geneSymbol	chr	strand	exonStart_0base	exonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	Adipose - Subcutaneous_ref_PSI	Adipose - Visceral (Omentum)_ref_PSI	Adrenal Gland_ref_PSI	Artery - Aorta_ref_PSI	Artery - Coronary_ref_PSI	Artery - Tibial_ref_PSI	Bladder_ref_PSI	Brain - Amygdala_ref_PSI	Brain - Anterior cingulate cortex (BA24)_ref_PSI	Brain - Caudate (basal ganglia)_ref_PSI	Brain - Cerebellar Hemisphere_ref_PSI	Brain - Cerebellum_ref_PSI	Brain - Cortex_ref_PSI	Brain - Frontal Cortex (BA9)_ref_PSI	Brain - Hippocampus_ref_PSI	Brain - Hypothalamus_ref_PSI	Brain - Nucleus accumbens (basal ganglia)_ref_PSI	Brain - Putamen (basal ganglia)_ref_PSI	Brain - Spinal cord (cervical c-1)_ref_PSI	Brain - Substantia nigra_ref_PSI	Breast - Mammary Tissue_ref_PSI	Cells - Cultured fibroblasts_ref_PSI	Cells - EBV-transformed lymphocytes_ref_PSI	Cervix - Ectocervix_ref_PSI	Cervix - Endocervix_ref_PSI	Colon - Sigmoid_ref_PSI	Colon - Transverse_ref_PSI	Esophagus - Gastroesophageal Junction_ref_PSI	Esophagus - Mucosa_ref_PSI	Esophagus - Muscularis_ref_PSI	Fallopian Tube_ref_PSI	Heart - Atrial Appendage_ref_PSI	Heart - Left Ventricle_ref_PSI	Kidney - Cortex_ref_PSI	Liver_ref_PSI	Lung_ref_PSI	Minor Salivary Gland_ref_PSI	Muscle - Skeletal_ref_PSI	Nerve - Tibial_ref_PSI	Ovary_ref_PSI	Pancreas_ref_PSI	Pituitary_ref_PSI	Prostate_ref_PSI	Skin - Not Sun Exposed (Suprapubic)_ref_PSI	Skin - Sun Exposed (Lower leg)_ref_PSI	Small Intestine - Terminal Ileum_ref_PSI	Spleen_ref_PSI	Stomach_ref_PSI	Testis_ref_PSI	Thyroid_ref_PSI	Uterus_ref_PSI	Vagina_ref_PSI	Whole Blood_ref_PSI	Adipose - Subcutaneous_deltaPSI	Adipose - Visceral (Omentum)_deltaPSI	Adrenal Gland_deltaPSI	Artery - Aorta_deltaPSI	Artery - Coronary_deltaPSI	Artery - Tibial_deltaPSI	Bladder_deltaPSI	Brain - Amygdala_deltaPSI	Brain - Anterior cingulate cortex (BA24)_deltaPSI	Brain - Caudate (basal ganglia)_deltaPSI	Brain - Cerebellar Hemisphere_deltaPSI	Brain - Cerebellum_deltaPSI	Brain - Cortex_deltaPSI	Brain - Frontal Cortex (BA9)_deltaPSI	Brain - Hippocampus_deltaPSI	Brain - Hypothalamus_deltaPSI	Brain - Nucleus accumbens (basal ganglia)_deltaPSI	Brain - Putamen (basal ganglia)_deltaPSI	Brain - Spinal cord (cervical c-1)_deltaPSI	Brain - Substantia nigra_deltaPSI	Breast - Mammary Tissue_deltaPSI	Cells - Cultured fibroblasts_deltaPSI	Cells - EBV-transformed lymphocytes_deltaPSI	Cervix - Ectocervix_deltaPSI	Cervix - Endocervix_deltaPSI	Colon - Sigmoid_deltaPSI	Colon - Transverse_deltaPSI	Esophagus - Gastroesophageal Junction_deltaPSI	Esophagus - Mucosa_deltaPSI	Esophagus - Muscularis_deltaPSI	Fallopian Tube_deltaPSI	Heart - Atrial Appendage_deltaPSI	Heart - Left Ventricle_deltaPSI	Kidney - Cortex_deltaPSI	Liver_deltaPSI	Lung_deltaPSI	Minor Salivary Gland_deltaPSI	Muscle - Skeletal_deltaPSI	Nerve - Tibial_deltaPSI	Ovary_deltaPSI	Pancreas_deltaPSI	Pituitary_deltaPSI	Prostate_deltaPSI	Skin - Not Sun Exposed (Suprapubic)_deltaPSI	Skin - Sun Exposed (Lower leg)_deltaPSI	Small Intestine - Terminal Ileum_deltaPSI	Spleen_deltaPSI	Stomach_deltaPSI	Testis_deltaPSI	Thyroid_deltaPSI	Uterus_deltaPSI	Vagina_deltaPSI	Whole Blood_deltaPSI
11_47369212_G_C_b37	0.0415	47369211	G	C	ENSG00000134571.10_2	MYBPC3	chr11	-	47368976	47369030	47368177	47368198	47369201	47369231	0.8497	0.8574	0.8544	0.8279	0.8405	0.8359	0.8289	0.8615	0.8621	0.8682	0.8274	0.8208	0.8486	0.8626	0.8648	0.8665	0.8512	0.8712	0.846	0.8688	0.8594	0.851	0.8732	0.8492	0.8482	0.8563	0.8675	0.8551	0.8384	0.845	0.8433	0.8584	0.8759	0.8584	0.883	0.8498	0.8602	0.851	0.8654	0.8492	0.8793	0.8712	0.8462	0.8577	0.8551	0.8714	0.893	0.875	0.8402	0.874	0.8356	0.8431	0.8747	0.0307	0.0302	0.0282	0.0342	0.0289	0.0287	0.0336	0.0244	0.0237	0.0229	0.0261	0.0287	0.0311	0.0224	0.0231	0.0225	0.0266	0.0243	0.0329	0.0229	0.0278	0.0328	0.0288	0.0258	0.028	0.0314	0.0335	0.0282	0.0415	0.0287	0.0284	0.0293	0.0239	0.03	0.0286	0.0311	0.0326	0.0272	0.0292	0.0261	0.0215	0.0239	0.0351	0.0321	0.0344	0.0247	0.02	0.0266	0.04	0.0156	0.0337	0.0295	0.029
11_47369212_G_C_b37	-0.3383	47369211	G	C	ENSG00000134571.10_2	MYBPC3	chr11	-	47369201	47369231	47368976	47369030	47369407	47369456	0.839	0.8344	0.8299	0.822	0.8219	0.7968	0.8307	0.818	0.817	0.8207	0.7236	0.7513	0.8097	0.8212	0.8254	0.8163	0.8183	0.8214	0.8376	0.8166	0.8544	0.7868	0.8149	0.8301	0.8091	0.8348	0.8299	0.8375	0.8355	0.8295	0.8236	0.8043	0.7973	0.8217	0.8336	0.8344	0.8528	0.7971	0.8224	0.7987	0.8464	0.8381	0.8384	0.8356	0.8355	0.8396	0.8432	0.8382	0.7605	0.8021	0.8142	0.8481	0.8321	-0.3105	-0.3283	-0.3103	-0.291	-0.2923	-0.2902	-0.2883	-0.3033	-0.2945	-0.284	-0.2349	-0.2443	-0.2752	-0.2754	-0.2977	-0.2802	-0.2795	-0.2962	-0.2929	-0.2902	-0.2851	-0.3211	-0.2998	-0.2784	-0.2792	-0.32	-0.3092	-0.3201	-0.3252	-0.327	-0.2575	-0.3381	-0.3383	-0.3326	-0.3135	-0.2762	-0.3185	-0.331	-0.2545	-0.2564	-0.2974	-0.2653	-0.2857	-0.2815	-0.283	-0.2728	-0.2413	-0.3314	-0.2552	-0.2802	-0.2601	-0.2814	-0.3211
11_47369212_G_C_b37	0.0111	47369211	G	C	ENSG00000134571.10_2	MYBPC3	chr11	-	47369407	47369456	47369201	47369231	47369974	47370092	0.9499	0.95	0.9609	0.9508	0.9527	0.9512	0.9565	0.9449	0.9356	0.9404	0.912	0.9122	0.9298	0.9293	0.9466	0.9395	0.9324	0.9457	0.9508	0.9491	0.9515	0.9571	0.9537	0.9566	0.9459	0.9569	0.9533	0.9555	0.9559	0.9551	0.9333	0.9453	0.9507	0.9527	0.9577	0.9439	0.95	0.9386	0.9389	0.9419	0.9585	0.9386	0.9523	0.9454	0.9453	0.9542	0.9587	0.9546	0.9155	0.9441	0.9469	0.9511	0.9539	0.0039	0.0035	0.0024	0.0051	0.0029	0.0036	0.004	0.0023	0.0064	0.0051	0.0033	0.002	0.0075	0.0068	0.0027	0.005	0.0061	0.004	0.0046	0.0048	0.0029	0.0055	0.0037	0.0017	0.0011	0.0052	0.0063	0.0069	0.007	0.0077	0.0086	0.0068	0.0069	0.0041	0.004	0.0053	0.005	0.01	0.0074	0.0091	0.0031	0.0065	0.0045	0.0067	0.0065	0.0065	0.0039	0.0032	0.0111	0.0057	0.0038	0.0041	0.0054
11_94219111_G_A_b37	-0.3088	94219110	G	A	ENSG00000020922.12_3	MRE11	chr11	-	94219089	94219250	94211926	94212042	94223998	94224131	0.6638	0.6536	0.6856	0.6819	0.6772	0.663	0.6898	0.6026	0.6257	0.6386	0.6033	0.6459	0.6592	0.6277	0.6231	0.6148	0.6044	0.6571	0.6444	0.6338	0.6587	0.6448	0.6046	0.6537	0.6442	0.7079	0.6749	0.7007	0.6763	0.7179	0.6368	0.6378	0.6413	0.6335	0.617	0.6488	0.6978	0.6295	0.6834	0.6118	0.6382	0.6254	0.6495	0.634	0.6476	0.6448	0.7065	0.6524	0.5949	0.6353	0.6318	0.6659	0.6323	-0.2699	-0.291	-0.2659	-0.2711	-0.2926	-0.2481	-0.2522	-0.2341	-0.2316	-0.2422	-0.1817	-0.1966	-0.2336	-0.2216	-0.2424	-0.2427	-0.2299	-0.2533	-0.2551	-0.2626	-0.2825	-0.267	-0.2456	-0.26	-0.2511	-0.2837	-0.2809	-0.2862	-0.29	-0.2889	-0.2385	-0.2929	-0.2927	-0.2768	-0.2721	-0.277	-0.3088	-0.2675	-0.2598	-0.2386	-0.2582	-0.2233	-0.2631	-0.295	-0.2874	-0.2693	-0.2693	-0.2738	-0.1693	-0.2674	-0.2393	-0.2776	-0.2531
11_94219111_G_A_b37	-0.1013	94219110	G	A	ENSG00000020922.12_3	MRE11	chr11	-	94219089	94219250	94212839	94212927	94223998	94224131	0.9452	0.9504	0.9496	0.9448	0.9501	0.9352	0.9349	0.9195	0.9189	0.9231	0.8398	0.8669	0.9194	0.9218	0.9202	0.9276	0.9138	0.925	0.9199	0.933	0.937	0.9471	0.9195	0.9186	0.9134	0.9394	0.9472	0.9449	0.9407	0.9479	0.9131	0.9509	0.9482	0.9348	0.942	0.9358	0.9514	0.9478	0.9116	0.8988	0.9391	0.9166	0.9259	0.9332	0.936	0.9393	0.9382	0.9446	0.8534	0.9086	0.9058	0.9261	0.9238	-0.0605	-0.0604	-0.0609	-0.0629	-0.0567	-0.0683	-0.0668	-0.0792	-0.0691	-0.0688	-0.1013	-0.0878	-0.0623	-0.0629	-0.0751	-0.0688	-0.0777	-0.0713	-0.0702	-0.0727	-0.0709	-0.0665	-0.0918	-0.0841	-0.0879	-0.0723	-0.0653	-0.0677	-0.0707	-0.0617	-0.0818	-0.0613	-0.0626	-0.0698	-0.0754	-0.0672	-0.0562	-0.0565	-0.0849	-0.0851	-0.0608	-0.0802	-0.0812	-0.0712	-0.07	-0.0669	-0.0623	-0.0641	-0.0984	-0.0952	-0.0886	-0.0737	-0.0772
11_94219111_G_A_b37	-0.0933	94219110	G	A	ENSG00000020922.12_3	MRE11	chr11	-	94219089	94219250	94212860	94212927	94223998	94224131	0.9513	0.9545	0.9557	0.9509	0.9555	0.9426	0.9434	0.925	0.9266	0.9294	0.8528	0.8779	0.9236	0.9264	0.9268	0.9332	0.9212	0.9325	0.9294	0.9385	0.9426	0.9548	0.9253	0.9277	0.9229	0.947	0.952	0.9504	0.9465	0.9534	0.9246	0.9561	0.9542	0.9415	0.9469	0.942	0.9563	0.9499	0.9207	0.9095	0.9453	0.9256	0.9316	0.9377	0.9424	0.9443	0.9427	0.9503	0.8643	0.9175	0.9159	0.9344	0.9318	-0.0512	-0.0493	-0.0524	-0.0539	-0.0484	-0.0586	-0.0594	-0.068	-0.065	-0.0619	-0.0933	-0.0821	-0.0589	-0.0611	-0.0658	-0.0618	-0.0698	-0.0651	-0.0617	-0.064	-0.0627	-0.0576	-0.0824	-0.0746	-0.0821	-0.0625	-0.0569	-0.0567	-0.0621	-0.0526	-0.0734	-0.0513	-0.0523	-0.0616	-0.0667	-0.0583	-0.0484	-0.0519	-0.077	-0.077	-0.0546	-0.0725	-0.0691	-0.0604	-0.0618	-0.0596	-0.0556	-0.0547	-0.0921	-0.0822	-0.0784	-0.0641	-0.0658
11_94219111_G_A_b37	-0.1929	94219110	G	A	ENSG00000020922.12_3	MRE11	chr11	-	94219089	94219250	94212908	94212927	94223998	94224131	0.864	0.8675	0.8837	0.8767	0.88	0.8612	0.8608	0.8504	0.8532	0.8569	0.7744	0.8023	0.8556	0.8453	0.856	0.8616	0.8405	0.8638	0.8612	0.8693	0.8606	0.8724	0.8129	0.8446	0.8371	0.8635	0.8807	0.8815	0.8742	0.8876	0.835	0.8974	0.8878	0.8679	0.8579	0.8614	0.8962	0.8501	0.8459	0.7855	0.8736	0.8408	0.8603	0.8602	0.8667	0.8651	0.8641	0.8815	0.7505	0.8321	0.821	0.8558	0.8272	-0.1687	-0.1724	-0.1308	-0.1603	-0.1447	-0.1541	-0.1638	-0.1518	-0.149	-0.1384	-0.1486	-0.128	-0.13	-0.1408	-0.1432	-0.1412	-0.146	-0.1376	-0.1521	-0.1516	-0.16	-0.1647	-0.1929	-0.1728	-0.1682	-0.1625	-0.152	-0.1486	-0.1689	-0.1445	-0.1725	-0.1462	-0.1429	-0.1511	-0.1754	-0.1551	-0.1514	-0.1525	-0.156	-0.1641	-0.1601	-0.1459	-0.1468	-0.1687	-0.1517	-0.1579	-0.1499	-0.1429	-0.1479	-0.1831	-0.1686	-0.1756	-0.1686
11_94219111_G_A_b37	-0.2786	94219110	G	A	ENSG00000020922.12_3	MRE11	chr11	-	94219089	94219250	94216935	94217005	94223998	94224131	0.746	0.7239	0.7774	0.7793	0.7713	0.7494	0.7751	0.7003	0.7067	0.7127	0.6447	0.675	0.7302	0.7074	0.7125	0.6979	0.6819	0.7323	0.7179	0.7223	0.7292	0.7311	0.6801	0.7373	0.7077	0.7742	0.7476	0.7741	0.728	0.7808	0.7362	0.7321	0.7466	0.7271	0.7168	0.7074	0.7709	0.7321	0.746	0.6566	0.7348	0.6685	0.723	0.726	0.7359	0.7188	0.7471	0.7514	0.6314	0.6989	0.7036	0.7633	0.7294	-0.2665	-0.2728	-0.2527	-0.2608	-0.277	-0.2561	-0.2584	-0.2248	-0.2039	-0.2177	-0.1693	-0.1724	-0.2077	-0.1986	-0.2276	-0.2162	-0.2054	-0.2262	-0.2238	-0.2302	-0.2599	-0.2507	-0.2331	-0.2542	-0.2514	-0.2473	-0.2558	-0.2512	-0.2532	-0.2362	-0.2455	-0.2534	-0.2506	-0.2599	-0.2664	-0.2539	-0.2786	-0.2363	-0.2492	-0.2097	-0.2409	-0.2116	-0.2458	-0.2756	-0.2545	-0.2417	-0.2241	-0.2506	-0.1666	-0.2518	-0.241	-0.2662	-0.2447
13_52535985_A_C_b37	-0.0765	52535984	A	C	ENSG00000123191.14_3	ATP7B	chr13	-	52535972	52536049	52531651	52534458	52539007	52539169	0.7471	0.7419	0.8106	0.728	0.7591	0.7099	0.7807	0.7235	0.7304	0.7336	0.7067	0.7061	0.7142	0.7438	0.7308	0.7398	0.7317	0.7393	0.7328	0.7461	0.7545	0.7838	0.7446	0.739	0.7467	0.7557	0.7969	0.7315	0.7848	0.7345	0.7595	0.7348	0.7623	0.7653	0.761	0.7553	0.7725	0.7774	0.717	0.7338	0.7516	0.7538	0.7725	0.7617	0.7481	0.7928	0.8091	0.7585	0.748	0.7958	0.7465	0.7501	0.7324	-0.0743	-0.0705	-0.0551	-0.0666	-0.0658	-0.0652	-0.0562	-0.0648	-0.0592	-0.0589	-0.0501	-0.0505	-0.0639	-0.0551	-0.0659	-0.0607	-0.0562	-0.0613	-0.0611	-0.0633	-0.068	-0.0639	-0.0542	-0.0712	-0.0603	-0.0617	-0.0527	-0.0675	-0.0668	-0.0739	-0.057	-0.076	-0.0661	-0.0757	-0.0765	-0.0677	-0.0626	-0.0591	-0.0695	-0.0578	-0.0639	-0.0571	-0.0632	-0.0606	-0.0674	-0.0574	-0.0631	-0.064	-0.053	-0.0561	-0.0672	-0.0647	-0.0651
13_52535985_A_C_b37	-0.0915	52535984	A	C	ENSG00000123191.14_3	ATP7B	chr13	-	52535972	52536049	52534283	52534458	52539007	52539169	0.7325	0.7081	0.7872	0.6928	0.7241	0.6823	0.7636	0.6804	0.6891	0.7068	0.6858	0.701	0.6891	0.7084	0.6908	0.7107	0.7061	0.7005	0.7113	0.7177	0.7422	0.7534	0.6952	0.7135	0.7322	0.7202	0.7547	0.7157	0.7724	0.7143	0.7385	0.7184	0.7495	0.7385	0.7298	0.7335	0.7675	0.7553	0.7004	0.6698	0.703	0.7273	0.7639	0.7437	0.7287	0.7523	0.7876	0.7385	0.717	0.7675	0.6957	0.7475	0.6293	-0.0884	-0.0841	-0.0632	-0.0815	-0.0848	-0.0746	-0.0747	-0.0678	-0.0629	-0.0677	-0.055	-0.0583	-0.0642	-0.0605	-0.0695	-0.0618	-0.0661	-0.0726	-0.0697	-0.0702	-0.0784	-0.077	-0.0653	-0.0753	-0.0761	-0.0866	-0.0749	-0.0915	-0.0731	-0.0899	-0.0697	-0.0796	-0.07	-0.0801	-0.0818	-0.0815	-0.0738	-0.0719	-0.0796	-0.0671	-0.0802	-0.0629	-0.0685	-0.0759	-0.0761	-0.0746	-0.0746	-0.0737	-0.0615	-0.0705	-0.0779	-0.0811	-0.079
14_73637762_A_G_b37	-0.0744	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614650	73614814	73640273	73640402	0.9141	0.9171	0.9357	0.9258	0.9258	0.9213	0.9047	0.927	0.9264	0.9297	0.8627	0.878	0.9306	0.9281	0.929	0.9295	0.9237	0.9344	0.921	0.9299	0.9023	0.9279	0.9165	0.8953	0.8927	0.9176	0.9277	0.916	0.9244	0.9167	0.8946	0.9426	0.9433	0.9376	0.9367	0.9063	0.9282	0.9438	0.8916	0.8972	0.9326	0.9177	0.8922	0.8962	0.898	0.9245	0.9216	0.9414	0.8664	0.8988	0.8847	0.8866	0.9178	-0.0509	-0.0482	-0.0398	-0.039	-0.0389	-0.0441	-0.056	-0.035	-0.0358	-0.0345	-0.0624	-0.0555	-0.0348	-0.0335	-0.0354	-0.0368	-0.0322	-0.0351	-0.0455	-0.0363	-0.051	-0.0453	-0.0591	-0.0575	-0.0577	-0.0492	-0.0473	-0.0427	-0.044	-0.043	-0.0534	-0.0421	-0.0382	-0.0447	-0.051	-0.0485	-0.0443	-0.04	-0.0585	-0.0744	-0.0474	-0.0487	-0.0461	-0.049	-0.0472	-0.0493	-0.0521	-0.0399	-0.0579	-0.0574	-0.0606	-0.0533	-0.0648
14_73637762_A_G_b37	-0.165	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614674	73614802	73640273	73640352	0.8276	0.832	0.8629	0.8516	0.8464	0.8278	0.8079	0.8411	0.8378	0.8555	0.7551	0.7968	0.8499	0.8465	0.8503	0.8467	0.8501	0.8579	0.8269	0.8407	0.8149	0.8062	0.803	0.8145	0.7941	0.8332	0.8511	0.8343	0.8461	0.8333	0.7987	0.8677	0.8647	0.8662	0.8569	0.8314	0.8612	0.8576	0.8009	0.7647	0.8437	0.8259	0.8057	0.7975	0.7948	0.8394	0.8159	0.8622	0.7273	0.7881	0.776	0.8051	0.8173	-0.1318	-0.14	-0.1202	-0.1193	-0.1146	-0.1312	-0.1437	-0.1331	-0.1081	-0.1062	-0.1119	-0.1151	-0.1025	-0.0975	-0.122	-0.1162	-0.1059	-0.1098	-0.1278	-0.1135	-0.1472	-0.165	-0.1546	-0.1422	-0.1326	-0.1277	-0.1402	-0.1268	-0.1328	-0.1209	-0.125	-0.123	-0.1047	-0.1166	-0.1223	-0.1284	-0.1161	-0.1213	-0.1523	-0.159	-0.1123	-0.1242	-0.1205	-0.1248	-0.128	-0.1298	-0.1328	-0.1142	-0.1187	-0.1231	-0.1387	-0.1349	-0.1524
14_73637762_A_G_b37	-0.1512	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614674	73614802	73640273	73640388	0.8334	0.8402	0.874	0.8563	0.8535	0.8368	0.8181	0.8482	0.8443	0.8578	0.7791	0.8115	0.8591	0.8537	0.8535	0.8563	0.8535	0.8597	0.8342	0.8465	0.8195	0.8236	0.8189	0.8166	0.8086	0.8448	0.8581	0.8466	0.8571	0.8452	0.8096	0.8723	0.8735	0.8727	0.8582	0.8418	0.8688	0.8612	0.8105	0.7897	0.8487	0.8395	0.8137	0.8112	0.8109	0.8497	0.8285	0.8692	0.7444	0.803	0.7867	0.8023	0.8149	-0.1236	-0.1326	-0.107	-0.112	-0.1139	-0.1239	-0.137	-0.1262	-0.1038	-0.1027	-0.1053	-0.106	-0.0948	-0.0883	-0.1148	-0.1094	-0.0939	-0.1029	-0.124	-0.1112	-0.1308	-0.1495	-0.1444	-0.1264	-0.1266	-0.1225	-0.1391	-0.117	-0.1333	-0.1167	-0.1193	-0.1205	-0.1053	-0.1172	-0.117	-0.114	-0.1127	-0.1155	-0.1412	-0.1512	-0.1166	-0.1117	-0.1124	-0.119	-0.1258	-0.1269	-0.1213	-0.1179	-0.1135	-0.1168	-0.1309	-0.1233	-0.1418
14_73637762_A_G_b37	-0.0755	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614674	73614802	73640273	73640415	0.9074	0.9104	0.9261	0.9212	0.9216	0.9155	0.8986	0.9225	0.9224	0.926	0.8545	0.8698	0.9265	0.9244	0.9253	0.9266	0.9199	0.9294	0.9146	0.9238	0.8964	0.9242	0.9052	0.8916	0.8881	0.9131	0.9199	0.9117	0.9164	0.912	0.8888	0.9366	0.938	0.9281	0.9309	0.903	0.9203	0.9373	0.8863	0.8859	0.9265	0.9097	0.8879	0.8885	0.8906	0.9164	0.911	0.9331	0.8555	0.8938	0.8804	0.8812	0.9092	-0.0518	-0.053	-0.0433	-0.0457	-0.0423	-0.0506	-0.0603	-0.0411	-0.041	-0.0382	-0.0683	-0.0604	-0.0435	-0.036	-0.0397	-0.0412	-0.0364	-0.039	-0.0508	-0.0403	-0.0547	-0.0521	-0.0638	-0.0603	-0.0637	-0.0511	-0.0499	-0.0453	-0.0509	-0.0463	-0.0567	-0.0499	-0.0434	-0.0511	-0.0555	-0.0488	-0.0485	-0.0462	-0.0606	-0.0755	-0.0486	-0.0543	-0.0499	-0.0488	-0.0496	-0.052	-0.0576	-0.0426	-0.0655	-0.0559	-0.0654	-0.0537	-0.0724
14_73637762_A_G_b37	-0.0739	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614674	73614814	73640273	73640415	0.9092	0.9107	0.9266	0.9208	0.9204	0.9183	0.8988	0.9235	0.9226	0.9266	0.8549	0.8721	0.9287	0.9262	0.9261	0.9279	0.9202	0.9299	0.9168	0.9256	0.8978	0.9248	0.9091	0.8912	0.8876	0.913	0.9188	0.912	0.9175	0.9127	0.8879	0.9372	0.9387	0.9283	0.9292	0.9024	0.9195	0.9395	0.8864	0.8857	0.9251	0.9083	0.8899	0.8888	0.8905	0.9158	0.9103	0.933	0.858	0.8909	0.8799	0.881	0.9094	-0.0512	-0.0501	-0.0448	-0.0429	-0.0401	-0.0481	-0.0614	-0.0392	-0.0386	-0.037	-0.065	-0.0601	-0.0408	-0.0349	-0.0387	-0.0388	-0.0348	-0.0364	-0.0478	-0.037	-0.0513	-0.0498	-0.0638	-0.0595	-0.0633	-0.0508	-0.051	-0.0462	-0.0477	-0.0459	-0.0558	-0.049	-0.0451	-0.0496	-0.0557	-0.0491	-0.0488	-0.0448	-0.0617	-0.0739	-0.048	-0.0502	-0.0505	-0.0493	-0.0497	-0.0519	-0.0569	-0.0416	-0.0627	-0.0553	-0.0646	-0.0516	-0.0715
14_73637762_A_G_b37	-0.1415	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614674	73614814	73640273	73640912	0.8602	0.8583	0.8798	0.8683	0.8753	0.866	0.8497	0.8726	0.8786	0.8794	0.7648	0.8009	0.8782	0.876	0.8774	0.8765	0.8766	0.8821	0.854	0.8746	0.8399	0.8666	0.8465	0.8082	0.8097	0.8585	0.874	0.8535	0.8643	0.8613	0.8247	0.8735	0.8829	0.8647	0.8752	0.8535	0.877	0.8816	0.8458	0.7932	0.8775	0.8477	0.8395	0.8278	0.8361	0.8767	0.8671	0.8855	0.7845	0.8299	0.8025	0.8244	0.8413	-0.103	-0.098	-0.0923	-0.1066	-0.1089	-0.1074	-0.1173	-0.1032	-0.0947	-0.085	-0.0942	-0.107	-0.0911	-0.0868	-0.0991	-0.0923	-0.0837	-0.089	-0.1163	-0.0996	-0.114	-0.1141	-0.1184	-0.1336	-0.1415	-0.1069	-0.1	-0.0993	-0.1044	-0.1018	-0.1178	-0.1025	-0.0967	-0.0997	-0.1041	-0.0928	-0.0983	-0.0976	-0.0947	-0.1404	-0.0929	-0.0965	-0.1044	-0.1049	-0.1082	-0.0914	-0.086	-0.0936	-0.1066	-0.1023	-0.1216	-0.1172	-0.1248
14_73637762_A_G_b37	-0.079	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614727	73614802	73640273	73640415	0.8986	0.898	0.9162	0.9095	0.912	0.9098	0.891	0.9112	0.9132	0.9151	0.845	0.8565	0.9179	0.9173	0.915	0.9182	0.9092	0.9176	0.9034	0.9126	0.887	0.9184	0.8932	0.8866	0.882	0.9058	0.9062	0.9033	0.9	0.9042	0.8833	0.9248	0.9261	0.9145	0.9229	0.8947	0.9073	0.9244	0.8799	0.8704	0.917	0.9017	0.8813	0.8728	0.8757	0.9031	0.8981	0.9164	0.8451	0.8821	0.8768	0.8687	0.8907	-0.0561	-0.059	-0.0528	-0.0533	-0.0483	-0.0545	-0.0675	-0.0484	-0.0437	-0.0425	-0.0701	-0.0631	-0.0442	-0.038	-0.0464	-0.0423	-0.0403	-0.0444	-0.0542	-0.048	-0.0585	-0.0604	-0.0683	-0.0661	-0.0634	-0.0591	-0.0585	-0.0494	-0.0585	-0.0516	-0.0597	-0.0573	-0.0546	-0.0569	-0.0568	-0.0515	-0.0582	-0.0545	-0.0684	-0.0747	-0.0539	-0.0576	-0.0559	-0.0561	-0.0558	-0.0597	-0.0588	-0.0474	-0.0695	-0.0591	-0.0674	-0.057	-0.079
14_73637762_A_G_b37	-0.075	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73614727	73614814	73640273	73640415	0.9013	0.8997	0.9163	0.9108	0.9128	0.9141	0.8927	0.915	0.9162	0.9181	0.8474	0.8613	0.9218	0.9202	0.9177	0.9216	0.9123	0.9195	0.9087	0.9171	0.8901	0.9176	0.9001	0.8858	0.8821	0.9071	0.9054	0.9043	0.9048	0.9064	0.883	0.9269	0.9269	0.9155	0.9222	0.8955	0.906	0.9303	0.8787	0.8724	0.9144	0.9006	0.8823	0.8755	0.8773	0.9031	0.897	0.9185	0.8502	0.8799	0.8777	0.8714	0.8919	-0.0526	-0.0538	-0.0529	-0.0523	-0.0457	-0.0518	-0.0661	-0.0453	-0.0429	-0.0406	-0.0676	-0.0623	-0.0434	-0.0358	-0.0437	-0.0413	-0.0388	-0.0393	-0.0519	-0.0431	-0.0556	-0.0554	-0.0676	-0.0615	-0.064	-0.0555	-0.0583	-0.0518	-0.0529	-0.0535	-0.06	-0.056	-0.055	-0.0523	-0.0553	-0.0517	-0.0525	-0.0536	-0.0663	-0.075	-0.0528	-0.0517	-0.055	-0.0528	-0.0537	-0.0579	-0.0574	-0.0456	-0.0661	-0.0595	-0.0674	-0.0535	-0.074
14_73637762_A_G_b37	-0.2253	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73626716	73626846	73640273	73640415	0.5149	0.4839	0.5241	0.5185	0.4904	0.4966	0.5222	0.4668	0.4756	0.4929	0.5082	0.5629	0.5014	0.4838	0.4646	0.452	0.4877	0.4894	0.4644	0.4764	0.5003	0.403	0.4704	0.5116	0.5069	0.4691	0.4683	0.4578	0.5242	0.4554	0.5267	0.4775	0.4974	0.4972	0.5066	0.5236	0.5071	0.4771	0.5374	0.5203	0.5242	0.572	0.5267	0.4944	0.4886	0.5066	0.5319	0.5158	0.4835	0.5561	0.4583	0.4832	0.4454	-0.2052	-0.201	-0.2092	-0.2253	-0.2069	-0.2045	-0.2159	-0.1952	-0.1873	-0.1983	-0.1391	-0.1556	-0.1924	-0.1781	-0.1921	-0.1753	-0.1877	-0.194	-0.1903	-0.1956	-0.1941	-0.1654	-0.1749	-0.2034	-0.1916	-0.1873	-0.1993	-0.1879	-0.2167	-0.186	-0.2066	-0.1996	-0.2042	-0.2045	-0.2071	-0.2003	-0.2025	-0.1934	-0.2013	-0.1988	-0.1937	-0.1884	-0.1988	-0.1822	-0.1749	-0.1992	-0.1853	-0.2123	-0.1301	-0.1965	-0.1687	-0.1926	-0.1826
14_73637762_A_G_b37	-0.1409	73637761	A	G	ENSG00000080815.18_3	PSEN1	chr14	+	73637504	73637755	73634536	73636169	73640273	73640415	0.8325	0.8221	0.8569	0.8471	0.8505	0.8284	0.8273	0.8112	0.8202	0.8237	0.76	0.8007	0.823	0.813	0.8123	0.8089	0.812	0.8206	0.8121	0.8189	0.8253	0.8076	0.8298	0.83	0.8169	0.8329	0.8335	0.8403	0.8517	0.8374	0.8168	0.8173	0.8319	0.8384	0.8254	0.8348	0.8544	0.8273	0.8107	0.8065	0.8252	0.8414	0.8451	0.8082	0.8236	0.8482	0.846	0.8437	0.7575	0.834	0.8003	0.8306	0.8194	-0.1122	-0.1311	-0.1205	-0.1143	-0.1148	-0.1152	-0.1225	-0.1285	-0.1168	-0.1138	-0.0937	-0.1012	-0.116	-0.1081	-0.1276	-0.1225	-0.1071	-0.1119	-0.1334	-0.1208	-0.1264	-0.1382	-0.1282	-0.1341	-0.1343	-0.1208	-0.129	-0.1109	-0.1241	-0.1163	-0.1341	-0.1262	-0.1153	-0.1101	-0.1323	-0.104	-0.1094	-0.1256	-0.1178	-0.124	-0.1085	-0.103	-0.1095	-0.1161	-0.1105	-0.1079	-0.1034	-0.1118	-0.0959	-0.1092	-0.1347	-0.1234	-0.1409
16_2098764_C_G_b37	-0.1324	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2097465	2098066	2100400	2100487	0.9324	0.9316	0.9438	0.9414	0.9382	0.9315	0.9404	0.9172	0.9193	0.9189	0.8725	0.8819	0.9059	0.9089	0.9174	0.9229	0.9112	0.923	0.9271	0.9274	0.9306	0.9333	0.9303	0.9284	0.9277	0.9303	0.9435	0.9378	0.9453	0.9388	0.9252	0.9336	0.9375	0.9423	0.9341	0.9354	0.9476	0.9329	0.9243	0.9137	0.9468	0.9224	0.9408	0.9313	0.9335	0.9404	0.9403	0.9473	0.8844	0.9355	0.9149	0.9344	0.9279	-0.0939	-0.0974	-0.0979	-0.0931	-0.0901	-0.0973	-0.087	-0.1039	-0.1132	-0.097	-0.1193	-0.1137	-0.1154	-0.13	-0.1	-0.1121	-0.1063	-0.0966	-0.1096	-0.0971	-0.0974	-0.1324	-0.1067	-0.094	-0.0968	-0.0982	-0.1041	-0.0999	-0.0888	-0.099	-0.117	-0.0888	-0.0871	-0.0853	-0.1052	-0.0967	-0.0874	-0.099	-0.1165	-0.1058	-0.0969	-0.0998	-0.0898	-0.1153	-0.1068	-0.0951	-0.0943	-0.0791	-0.1141	-0.1043	-0.1098	-0.098	-0.102
16_2098764_C_G_b37	-0.1268	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2097989	2098066	2100400	2100487	0.9285	0.9246	0.9322	0.9371	0.932	0.9286	0.9402	0.9013	0.8955	0.8993	0.8703	0.8833	0.8827	0.8905	0.9014	0.9049	0.8905	0.9057	0.9096	0.9148	0.923	0.9303	0.9313	0.9286	0.9294	0.9309	0.9453	0.9328	0.9354	0.9335	0.9198	0.9243	0.9291	0.9339	0.9266	0.9276	0.9493	0.9236	0.9221	0.9148	0.939	0.9199	0.9306	0.9275	0.9282	0.9417	0.9396	0.9404	0.8888	0.9319	0.922	0.9319	0.9244	-0.0873	-0.0974	-0.109	-0.0951	-0.0954	-0.1006	-0.0788	-0.11	-0.1112	-0.1	-0.1175	-0.1063	-0.1113	-0.123	-0.106	-0.1096	-0.1083	-0.0996	-0.107	-0.1026	-0.0897	-0.1268	-0.1008	-0.0956	-0.0944	-0.0952	-0.1043	-0.0914	-0.0918	-0.095	-0.108	-0.1009	-0.1016	-0.0926	-0.106	-0.0924	-0.0862	-0.1084	-0.1108	-0.0969	-0.1015	-0.1047	-0.0958	-0.0991	-0.1017	-0.0966	-0.0927	-0.0845	-0.1032	-0.1056	-0.0958	-0.0898	-0.1009
16_2098764_C_G_b37	-0.127	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2097990	2098066	2100400	2100487	0.9284	0.9241	0.9321	0.9372	0.9318	0.9291	0.9401	0.9005	0.8948	0.8988	0.8705	0.8831	0.8817	0.8902	0.9011	0.904	0.8902	0.9051	0.9096	0.9144	0.9232	0.9307	0.9319	0.9285	0.9298	0.9309	0.9452	0.933	0.9347	0.9334	0.92	0.9238	0.9288	0.9337	0.9257	0.9271	0.9487	0.9241	0.9232	0.9149	0.9384	0.9197	0.9308	0.9275	0.928	0.9411	0.9393	0.9397	0.8889	0.9321	0.9223	0.9316	0.924	-0.0878	-0.0992	-0.1097	-0.0963	-0.0964	-0.1019	-0.0798	-0.1117	-0.112	-0.1009	-0.1164	-0.105	-0.112	-0.1246	-0.1075	-0.1109	-0.1089	-0.101	-0.1066	-0.1042	-0.0909	-0.127	-0.1012	-0.0954	-0.0956	-0.0968	-0.1051	-0.0933	-0.092	-0.0963	-0.1086	-0.1028	-0.1034	-0.094	-0.1084	-0.0928	-0.0871	-0.1095	-0.1117	-0.0966	-0.1028	-0.1055	-0.0973	-0.0998	-0.102	-0.0975	-0.0931	-0.0864	-0.1027	-0.1069	-0.0961	-0.0905	-0.1023
16_2098764_C_G_b37	-0.1343	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2098014	2098066	2100400	2100487	0.923	0.9249	0.9289	0.9319	0.9274	0.9268	0.9352	0.8992	0.8993	0.9019	0.866	0.8771	0.8844	0.8912	0.9014	0.9037	0.8909	0.9094	0.9122	0.914	0.9193	0.9243	0.9219	0.9226	0.9271	0.9269	0.9418	0.9313	0.9345	0.9317	0.9147	0.9252	0.9295	0.9331	0.9259	0.9242	0.9458	0.9279	0.9218	0.9091	0.9391	0.9177	0.9266	0.9234	0.9246	0.9404	0.9389	0.9392	0.8758	0.9297	0.9136	0.926	0.9251	-0.0945	-0.104	-0.1185	-0.0997	-0.1012	-0.1098	-0.087	-0.1094	-0.1123	-0.0992	-0.1247	-0.1126	-0.1076	-0.1267	-0.1038	-0.1083	-0.1096	-0.0966	-0.1095	-0.0983	-0.0961	-0.1343	-0.1139	-0.1035	-0.1044	-0.0977	-0.1088	-0.0988	-0.0988	-0.102	-0.1138	-0.102	-0.0967	-0.0964	-0.1052	-0.0984	-0.0897	-0.1118	-0.1223	-0.1057	-0.104	-0.1085	-0.1005	-0.1086	-0.1085	-0.0992	-0.0901	-0.0863	-0.112	-0.1183	-0.1102	-0.1016	-0.1004
16_2098764_C_G_b37	-0.1271	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2098020	2098066	2100400	2100487	0.9263	0.9253	0.9279	0.9353	0.9316	0.9287	0.9407	0.9023	0.9003	0.9038	0.8702	0.8793	0.885	0.8891	0.9046	0.9064	0.8924	0.9098	0.914	0.9172	0.9226	0.9301	0.9247	0.9266	0.93	0.93	0.9427	0.933	0.9363	0.9335	0.9201	0.9241	0.9295	0.9341	0.9264	0.9264	0.9463	0.9276	0.9229	0.9135	0.9408	0.9195	0.9274	0.9249	0.9263	0.9419	0.9412	0.9395	0.8809	0.9307	0.9191	0.9279	0.9263	-0.0889	-0.1002	-0.1131	-0.095	-0.0953	-0.1017	-0.0832	-0.1075	-0.1067	-0.099	-0.1212	-0.1054	-0.1034	-0.121	-0.1028	-0.1079	-0.1048	-0.0959	-0.109	-0.095	-0.0906	-0.1271	-0.1076	-0.0978	-0.0987	-0.0939	-0.1046	-0.0939	-0.0955	-0.0985	-0.1075	-0.0998	-0.0963	-0.0934	-0.1011	-0.0928	-0.0845	-0.1105	-0.1123	-0.0985	-0.1018	-0.1023	-0.0958	-0.1055	-0.1035	-0.0943	-0.086	-0.0825	-0.1067	-0.1132	-0.1005	-0.093	-0.0977
16_2098764_C_G_b37	-0.1339	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2098033	2098066	2100400	2100487	0.9209	0.9131	0.9119	0.9287	0.922	0.9196	0.9333	0.8968	0.8879	0.8993	0.8618	0.8743	0.8719	0.8771	0.8988	0.8961	0.8869	0.906	0.9108	0.9109	0.9167	0.9244	0.921	0.9181	0.9221	0.926	0.9397	0.9282	0.9248	0.9262	0.9092	0.9172	0.9206	0.9209	0.9113	0.9174	0.9398	0.9115	0.9176	0.898	0.9301	0.9039	0.917	0.9179	0.9204	0.9386	0.9351	0.9335	0.8801	0.915	0.9138	0.9225	0.9127	-0.1063	-0.1076	-0.123	-0.1016	-0.1002	-0.1083	-0.0907	-0.1155	-0.1137	-0.107	-0.1242	-0.1082	-0.1097	-0.1245	-0.1081	-0.1141	-0.1144	-0.1076	-0.1076	-0.1028	-0.1034	-0.1339	-0.1194	-0.1053	-0.1039	-0.1097	-0.107	-0.1061	-0.0978	-0.1041	-0.116	-0.1151	-0.1095	-0.0988	-0.1087	-0.1028	-0.0904	-0.1145	-0.1278	-0.1063	-0.1122	-0.1101	-0.1124	-0.1108	-0.1073	-0.1018	-0.0926	-0.0858	-0.0994	-0.1176	-0.108	-0.107	-0.1041
16_2098764_C_G_b37	-0.1588	2098763	C	G	ENSG00000103197.16_3	TSC2	chr16	+	2098587	2098754	2098202	2098274	2100400	2100487	0.936	0.9375	0.9378	0.9306	0.934	0.9207	0.9301	0.9075	0.9015	0.9105	0.851	0.8649	0.8876	0.8812	0.9065	0.8942	0.8969	0.919	0.9111	0.9124	0.9343	0.9158	0.9123	0.9182	0.9197	0.9282	0.943	0.9354	0.9459	0.9353	0.9229	0.9295	0.9321	0.9411	0.9359	0.9342	0.9492	0.9221	0.9259	0.911	0.9435	0.9276	0.9395	0.9379	0.9404	0.9456	0.9435	0.9508	0.864	0.9431	0.9095	0.9355	0.936	-0.0992	-0.1049	-0.1169	-0.1154	-0.1036	-0.1094	-0.1032	-0.1463	-0.1483	-0.1397	-0.1327	-0.1374	-0.1484	-0.1504	-0.1424	-0.1501	-0.1492	-0.1426	-0.1247	-0.1384	-0.1027	-0.1588	-0.1388	-0.1014	-0.1092	-0.1085	-0.1077	-0.1036	-0.095	-0.1142	-0.1075	-0.1213	-0.1252	-0.1125	-0.1245	-0.1028	-0.0894	-0.1366	-0.1129	-0.1166	-0.1044	-0.1154	-0.0896	-0.0996	-0.1016	-0.0889	-0.0818	-0.1017	-0.1125	-0.1046	-0.1174	-0.0895	-0.1255
2_110905531_C_T_b37	-0.212	110905530	C	T	ENSG00000144061.12_3	NPHP1	chr2	-	110905492	110905603	110904329	110904412	110907758	110907833	0.7758	0.7872	0.8415	0.7778	0.7993	0.7818	0.8017	0.8197	0.8343	0.8334	0.7182	0.7391	0.8373	0.8266	0.8341	0.8277	0.8253	0.8325	0.8105	0.8217	0.7844	0.7704	0.7626	0.7654	0.7512	0.784	0.8196	0.8025	0.8272	0.8127	0.7874	0.8274	0.8422	0.8438	0.8397	0.7695	0.8175	0.8042	0.756	0.6931	0.828	0.788	0.7918	0.8103	0.8211	0.7893	0.7903	0.8243	0.7273	0.7366	0.7346	0.7811	0.7928	-0.2073	-0.1943	-0.1897	-0.2048	-0.212	-0.209	-0.1955	-0.1662	-0.1572	-0.1486	-0.1576	-0.1693	-0.1381	-0.1415	-0.1568	-0.1523	-0.1498	-0.153	-0.1707	-0.1642	-0.2007	-0.1854	-0.1927	-0.1923	-0.1912	-0.19	-0.2038	-0.2005	-0.1971	-0.1906	-0.1882	-0.1879	-0.1752	-0.1708	-0.1885	-0.2108	-0.1822	-0.19	-0.2075	-0.1762	-0.1764	-0.1918	-0.2055	-0.1908	-0.1923	-0.1976	-0.1957	-0.1582	-0.1702	-0.2018	-0.1938	-0.1914	-0.1775
2_166854706_G_C_b37	-0.2885	166854705	G	C	ENSG00000144285.17_3	SCN1A	chr2	-	166854547	166854685	166852522	166852627	166856232	166856286	0.7756	0.7837	0.7956	0.7727	0.7808	0.7448	0.7684	0.7681	0.7593	0.7895	0.7157	0.7424	0.7549	0.7605	0.7767	0.7552	0.7561	0.7932	0.7845	0.7785	0.7697	0.7724	0.6987	0.7309	0.7438	0.7766	0.8157	0.7922	0.8082	0.8148	0.7803	0.7766	0.7926	0.7959	0.7932	0.7706	0.8105	0.7811	0.7802	0.6806	0.7746	0.7571	0.7836	0.7491	0.7573	0.809	0.8099	0.7985	0.7039	0.7653	0.7369	0.7531	0.755	-0.2494	-0.2301	-0.2569	-0.2339	-0.2366	-0.2583	-0.2412	-0.2627	-0.2518	-0.2475	-0.1942	-0.2055	-0.2188	-0.2011	-0.2649	-0.2506	-0.2466	-0.256	-0.2514	-0.2591	-0.2451	-0.2643	-0.2471	-0.2258	-0.2459	-0.2298	-0.2545	-0.2503	-0.2443	-0.2402	-0.235	-0.2679	-0.2469	-0.2605	-0.2874	-0.2294	-0.2885	-0.245	-0.233	-0.2597	-0.2618	-0.2276	-0.2293	-0.2511	-0.2606	-0.2445	-0.214	-0.2662	-0.1909	-0.246	-0.239	-0.232	-0.2609
2_166854706_G_C_b37	-0.2001	166854705	G	C	ENSG00000144285.17_3	SCN1A	chr2	-	166854547	166854685	166852562	166852627	166856232	166856573	0.8691	0.8771	0.8893	0.8789	0.8798	0.8653	0.8662	0.8751	0.8729	0.8731	0.7954	0.8017	0.86	0.8556	0.8761	0.8514	0.8617	0.8778	0.866	0.8667	0.8573	0.8636	0.8646	0.8483	0.863	0.8791	0.9029	0.8838	0.9014	0.8907	0.882	0.8645	0.8686	0.885	0.863	0.8632	0.8998	0.8737	0.8518	0.8272	0.8893	0.8482	0.8832	0.8802	0.8852	0.8997	0.8927	0.896	0.8353	0.8868	0.8612	0.8614	0.8787	-0.1609	-0.1637	-0.167	-0.1481	-0.1436	-0.1856	-0.1785	-0.1781	-0.1691	-0.1723	-0.1615	-0.1508	-0.1593	-0.1487	-0.1733	-0.1768	-0.1885	-0.1759	-0.1785	-0.1782	-0.1588	-0.1998	-0.1801	-0.1865	-0.1665	-0.1538	-0.1272	-0.1527	-0.15	-0.1492	-0.1646	-0.2001	-0.195	-0.1667	-0.185	-0.1521	-0.1509	-0.1667	-0.1637	-0.1913	-0.155	-0.1669	-0.1585	-0.1427	-0.1423	-0.1368	-0.1428	-0.1499	-0.1457	-0.1585	-0.1774	-0.1497	-0.1708
5_112102045_G_T_b37	-0.4181	112102044	G	T	ENSG00000134982.16_3	APC	chr5	+	112102022	112102107	112043218	112043579	112102885	112103087	0.9709	0.9738	0.9726	0.9705	0.972	0.9653	0.967	0.9728	0.9694	0.9718	0.9309	0.9372	0.9693	0.9648	0.9731	0.9709	0.9663	0.9743	0.9706	0.9751	0.9706	0.9678	0.9596	0.9692	0.9654	0.9688	0.9774	0.9743	0.9714	0.9756	0.9683	0.9768	0.9754	0.9796	0.9815	0.9696	0.9764	0.9724	0.9673	0.9623	0.9806	0.9637	0.9726	0.9702	0.9698	0.9755	0.9726	0.9798	0.9436	0.9678	0.9631	0.9674	0.9702	-0.3412	-0.3469	-0.3623	-0.3958	-0.3609	-0.3676	-0.3464	-0.3885	-0.3886	-0.3446	-0.3204	-0.3341	-0.3393	-0.349	-0.3744	-0.3651	-0.3539	-0.3542	-0.3318	-0.361	-0.3377	-0.3786	-0.4181	-0.348	-0.3531	-0.3412	-0.321	-0.3295	-0.3913	-0.3222	-0.3467	-0.3581	-0.3478	-0.3216	-0.2959	-0.3488	-0.3254	-0.3417	-0.3672	-0.3677	-0.3139	-0.274	-0.2868	-0.4018	-0.402	-0.3211	-0.3125	-0.33	-0.302	-0.3319	-0.3815	-0.3781	-0.4039
5_112102045_G_T_b37	-0.2126	112102044	G	T	ENSG00000134982.16_3	APC	chr5	+	112102022	112102107	112090569	112090722	112102885	112103019	0.9809	0.9811	0.9827	0.9826	0.9835	0.9786	0.9762	0.9781	0.974	0.9769	0.9439	0.9507	0.9698	0.9672	0.9782	0.974	0.9727	0.9795	0.979	0.9788	0.9818	0.9815	0.973	0.9791	0.9767	0.9816	0.9835	0.9841	0.9851	0.9856	0.9778	0.984	0.9844	0.9829	0.9856	0.9802	0.9837	0.9832	0.9754	0.9763	0.9868	0.9757	0.9795	0.9815	0.982	0.98	0.9812	0.9852	0.9537	0.9772	0.9751	0.978	0.9816	-0.1638	-0.1756	-0.159	-0.1916	-0.1724	-0.1813	-0.1824	-0.189	-0.1869	-0.1736	-0.2126	-0.1878	-0.1656	-0.1678	-0.1763	-0.186	-0.1859	-0.1685	-0.1741	-0.1751	-0.1651	-0.1598	-0.2	-0.1958	-0.1757	-0.176	-0.1382	-0.1719	-0.1576	-0.1633	-0.1776	-0.1657	-0.1513	-0.1545	-0.1413	-0.1643	-0.1558	-0.1638	-0.197	-0.1722	-0.1311	-0.135	-0.157	-0.1768	-0.1767	-0.143	-0.149	-0.139	-0.1903	-0.1677	-0.2038	-0.1839	-0.1888
5_112102045_G_T_b37	-0.2117	112102044	G	T	ENSG00000134982.16_3	APC	chr5	+	112102022	112102107	112090569	112090722	112102885	112103087	0.9817	0.9822	0.9837	0.9831	0.9838	0.9789	0.9771	0.9807	0.9765	0.9788	0.9427	0.9489	0.9731	0.9707	0.9804	0.9769	0.9751	0.9816	0.9808	0.9812	0.9824	0.9819	0.9728	0.9791	0.9767	0.9828	0.9845	0.9846	0.986	0.9856	0.9769	0.9847	0.9855	0.9856	0.9868	0.9807	0.9855	0.9839	0.9751	0.977	0.9878	0.9764	0.981	0.9826	0.9831	0.9813	0.9824	0.9867	0.9544	0.9775	0.9752	0.9798	0.9835	-0.1609	-0.1766	-0.17	-0.198	-0.177	-0.189	-0.1775	-0.1872	-0.1883	-0.1711	-0.2117	-0.1949	-0.1714	-0.1716	-0.1787	-0.1822	-0.1828	-0.1691	-0.1751	-0.173	-0.1645	-0.1642	-0.2044	-0.1988	-0.1757	-0.1758	-0.1408	-0.1755	-0.1552	-0.1612	-0.179	-0.1709	-0.1566	-0.1592	-0.147	-0.1711	-0.1531	-0.1676	-0.1983	-0.1704	-0.1303	-0.1391	-0.1577	-0.1739	-0.1753	-0.1531	-0.151	-0.14	-0.1914	-0.1727	-0.207	-0.1838	-0.1891
8_68066380_C_G_b37	-0.1084	68066379	C	G	ENSG00000104218.14_2	CSPP1	chr8	+	68066258	68066371	68049690	68049838	68070681	68070831	0.9041	0.9068	0.9213	0.9144	0.9158	0.8918	0.8998	0.9202	0.9176	0.9191	0.8221	0.8395	0.9101	0.9162	0.9192	0.925	0.917	0.9196	0.927	0.9285	0.9086	0.9115	0.8547	0.8959	0.8965	0.911	0.9277	0.9053	0.9221	0.909	0.8941	0.9274	0.9281	0.9237	0.9201	0.891	0.9226	0.9322	0.9016	0.8858	0.9264	0.8806	0.888	0.9084	0.9112	0.9204	0.9238	0.9277	0.8439	0.8981	0.8839	0.9072	0.8997	-0.0821	-0.0807	-0.0773	-0.0852	-0.0856	-0.0895	-0.0763	-0.0639	-0.0639	-0.0621	-0.0929	-0.0839	-0.0691	-0.0689	-0.0654	-0.0652	-0.0621	-0.0633	-0.0668	-0.0633	-0.0835	-0.0888	-0.104	-0.0843	-0.0872	-0.0889	-0.0746	-0.0892	-0.0715	-0.081	-0.0815	-0.0689	-0.073	-0.0756	-0.0763	-0.0914	-0.078	-0.0604	-0.0873	-0.0985	-0.0669	-0.0932	-0.1084	-0.0797	-0.0756	-0.074	-0.0744	-0.0722	-0.0894	-0.1035	-0.0849	-0.0807	-0.0915
8_68066380_C_G_b37	-0.0936	68066379	C	G	ENSG00000104218.14_2	CSPP1	chr8	+	68066258	68066371	68062017	68062170	68070681	68070831	0.9305	0.9361	0.9374	0.9379	0.9399	0.913	0.9241	0.9416	0.938	0.9406	0.8442	0.8618	0.9341	0.935	0.9387	0.9405	0.939	0.9413	0.9459	0.949	0.9336	0.9319	0.8876	0.9217	0.9207	0.9337	0.9469	0.9325	0.9438	0.9311	0.9222	0.9424	0.9406	0.944	0.9431	0.9188	0.938	0.9493	0.927	0.9059	0.9414	0.9006	0.9228	0.9262	0.9301	0.9421	0.9437	0.9459	0.8462	0.927	0.9111	0.929	0.9223	-0.0544	-0.0594	-0.0646	-0.0636	-0.0623	-0.0777	-0.0616	-0.0548	-0.0531	-0.0507	-0.0788	-0.071	-0.0572	-0.0545	-0.0551	-0.055	-0.0552	-0.0518	-0.0577	-0.0497	-0.0577	-0.0721	-0.0936	-0.0735	-0.0788	-0.0656	-0.0571	-0.0654	-0.0604	-0.0607	-0.0688	-0.0598	-0.0598	-0.062	-0.0628	-0.0734	-0.0645	-0.048	-0.0708	-0.0888	-0.0617	-0.0796	-0.0755	-0.0671	-0.06	-0.0601	-0.0571	-0.0585	-0.0841	-0.0774	-0.0804	-0.0617	-0.07
X_135112295_G_A_b37	-0.204	135112294	G	A	ENSG00000198689.10_3	SLC9A6	chrX	+	135112290	135112321	135106488	135106642	135115572	135115652	0.3728	0.3847	0.4476	0.3724	0.3846	0.3672	0.4182	0.395	0.4288	0.4279	0.4523	0.4676	0.4551	0.4421	0.4042	0.4181	0.4253	0.4256	0.4192	0.4107	0.379	0.3501	0.3288	0.4004	0.409	0.3636	0.3831	0.3685	0.436	0.3686	0.4006	0.3767	0.4073	0.3809	0.4095	0.4009	0.3892	0.4539	0.4034	0.3834	0.4257	0.4419	0.4064	0.4353	0.4428	0.389	0.4388	0.4047	0.4071	0.3791	0.3663	0.4139	0.4068	-0.165	-0.1612	-0.1943	-0.1591	-0.1676	-0.1576	-0.1829	-0.1606	-0.166	-0.1652	-0.1451	-0.1606	-0.1693	-0.1643	-0.1616	-0.1612	-0.1629	-0.1698	-0.1565	-0.1651	-0.1628	-0.1512	-0.1402	-0.1571	-0.1669	-0.1513	-0.1736	-0.1589	-0.1695	-0.1539	-0.1582	-0.165	-0.1816	-0.1666	-0.1762	-0.1817	-0.1669	-0.1838	-0.1637	-0.1587	-0.1789	-0.1782	-0.1791	-0.2025	-0.204	-0.1759	-0.1752	-0.1734	-0.13	-0.1595	-0.1455	-0.1769	-0.1524
X_135112295_G_A_b37	-0.1874	135112294	G	A	ENSG00000198689.10_3	SLC9A6	chrX	+	135112290	135112321	135106614	135106642	135122202	135122243	0.4019	0.4063	0.4462	0.3971	0.4093	0.4044	0.4355	0.4249	0.4569	0.4522	0.4109	0.4202	0.4648	0.4696	0.4319	0.4662	0.4618	0.454	0.4183	0.4378	0.4004	0.3547	0.3966	0.4029	0.4061	0.4101	0.4088	0.3907	0.4051	0.3837	0.4027	0.4222	0.4753	0.4189	0.4533	0.4103	0.4198	0.4674	0.3855	0.3607	0.4622	0.4246	0.4209	0.4237	0.422	0.4277	0.4451	0.4352	0.4392	0.3908	0.379	0.3912	0.4567	-0.1689	-0.1641	-0.164	-0.1631	-0.1659	-0.1644	-0.1619	-0.1491	-0.1483	-0.1389	-0.1301	-0.1291	-0.1526	-0.151	-0.1479	-0.142	-0.1395	-0.1527	-0.1435	-0.1511	-0.1654	-0.1486	-0.1564	-0.1556	-0.1504	-0.1477	-0.1597	-0.1489	-0.1583	-0.1445	-0.1479	-0.169	-0.1874	-0.1536	-0.1691	-0.1654	-0.1633	-0.1549	-0.1462	-0.1382	-0.1761	-0.144	-0.1565	-0.171	-0.1689	-0.1705	-0.1614	-0.1526	-0.1306	-0.1357	-0.1305	-0.1505	-0.1646
X_135112295_G_A_b37	-0.2126	135112294	G	A	ENSG00000198689.10_3	SLC9A6	chrX	+	135112290	135112321	135111044	135111134	135115572	135115652	0.4691	0.4679	0.5036	0.4799	0.4977	0.4613	0.5023	0.461	0.4685	0.4854	0.4846	0.4866	0.4754	0.4802	0.4658	0.4721	0.4767	0.494	0.4983	0.4768	0.4639	0.403	0.3944	0.4843	0.4922	0.4727	0.4837	0.4567	0.5076	0.4619	0.4813	0.4689	0.4928	0.4758	0.5026	0.497	0.5046	0.4909	0.475	0.452	0.5321	0.4947	0.4895	0.512	0.5188	0.4956	0.5279	0.513	0.4663	0.4639	0.4572	0.476	0.518	-0.1959	-0.1926	-0.1996	-0.1833	-0.1953	-0.1698	-0.2009	-0.1777	-0.1801	-0.1761	-0.1348	-0.1451	-0.182	-0.1782	-0.1772	-0.1802	-0.1732	-0.1828	-0.1785	-0.1874	-0.189	-0.1707	-0.1622	-0.175	-0.1848	-0.1764	-0.2026	-0.1771	-0.1912	-0.1806	-0.1774	-0.1895	-0.207	-0.2051	-0.2037	-0.1998	-0.2035	-0.1921	-0.1905	-0.1669	-0.2066	-0.1786	-0.2047	-0.204	-0.2057	-0.2076	-0.2062	-0.2069	-0.1338	-0.1872	-0.1635	-0.1843	-0.2126
X_135112295_G_A_b37	-0.2213	135112294	G	A	ENSG00000198689.10_3	SLC9A6	chrX	+	135112290	135112321	135111601	135112052	135115572	135115652	0.4547	0.4363	0.4738	0.4331	0.4556	0.4266	0.4892	0.4123	0.4389	0.4307	0.4776	0.5136	0.4659	0.4781	0.4143	0.425	0.4361	0.4301	0.4285	0.4188	0.4527	0.4236	0.408	0.4404	0.4545	0.4656	0.485	0.4518	0.5094	0.4539	0.4473	0.4284	0.4554	0.4314	0.4929	0.4588	0.4804	0.4532	0.4829	0.4585	0.5024	0.4871	0.4706	0.4943	0.51	0.4898	0.4967	0.4721	0.4887	0.4848	0.4524	0.4691	0.4673	-0.188	-0.1777	-0.1919	-0.1866	-0.1908	-0.168	-0.2022	-0.1473	-0.1552	-0.15	-0.1321	-0.1567	-0.1611	-0.1635	-0.1487	-0.1551	-0.1483	-0.1533	-0.1585	-0.1512	-0.1878	-0.1821	-0.1566	-0.1733	-0.168	-0.1769	-0.1987	-0.1829	-0.2149	-0.179	-0.1854	-0.1597	-0.1722	-0.1744	-0.1905	-0.1981	-0.2123	-0.1651	-0.1866	-0.1637	-0.1835	-0.1794	-0.1935	-0.2118	-0.2213	-0.2019	-0.1844	-0.1852	-0.1346	-0.1932	-0.1602	-0.1945	-0.1682

Predicting splicing levels of AS events

Option 1. User-provided AS events

The pre-compiled AS events and RBP expression levels across 53 GTEx tissues will be used for prediction.
iDARTS can make predictions for SE, A3SS, and A5SS. The format of each AS type can be found in rmats-turbo. More specifically:
- Shared columns:
  - ID: rMATS event id
  - GeneID: Gene id
  - geneSymbol: Gene name
  - chr: Chromosome
  - strand: Strand of the gene
- SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
  - The inclusion form includes the target exon (exonStart_0base, exonEnd)
- A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
  - The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
Process the AS events and make predicts on the AS events

# Build sequence features for user-provided AS events
./bin/iDARTS build_feature -i ./example/example.SE_events.txt -t SE -o ./example/example.SE_events.feature
# Predict splicing levels based on the sequence features and RBP expression levels across 53 GTEx tissues
./bin/iDARTS predict -i ./example/example.SE_events.feature -o ./example/example.SE_events.PSI.txt

Option 2. User-provided AS events, and RBP expression levels for specific sample types of interest

The preparation of AS events can be found in the above Option 1.
iDARTS can make predictions for specific sample types of interest. This is enabled by preparing input gene expression file (TPM values quantified by Kallisto).
The format of gene expression file:
- Column Name
  - GeneID: Gene id
  - Sample1,Sample2,Sample3,...: Expression levels of different samples separated by comma
Process the AS events and make predicts on the AS events

# Build sequence features for user-provided AS events
./bin/iDARTS build_feature -i ./example/example.SE_events.txt -t SE -o ./example/example.SE_events.feature
# Predict splicing levels based on the sequence features and user-provided RBP expression levels
./bin/iDARTS predict -i ./example/example.SE_events.feature -e ./example/example.RBP_expression_in_tissues.txt -o ./example/example.SE_events.PSI.txt

Output format:

iDARTS Prediction columns: (Suppose we have three samples with sample name Sample1, Sample2, and Sample3 specified in user-provided RBP expression levels of sample types. When not provided, the RBP expression levels across 53 GTEx tissues will be used.)

ID: AS event ID
Sample1: The predicted PSI of the target AS event in Sample1
Sample2: The predicted PSI of the target AS event in Sample2
Sample3: The predicted PSI of the target AS event in Sample3

Example output:

ID	Adipose - Subcutaneous	Adipose - Visceral (Omentum)	Adrenal Gland	Artery - Aorta	Artery - Coronary	Artery - Tibial	Bladder	Brain - Amygdala	Brain - Anterior cingulate cortex (BA24)	Brain - Caudate (basal ganglia)	Brain - Cerebellar Hemisphere	Brain - Cerebellum	Brain - Cortex	Brain - Frontal Cortex (BA9)	Brain - Hippocampus	Brain - Hypothalamus	Brain - Nucleus accumbens (basal ganglia)	Brain - Putamen (basal ganglia)	Brain - Spinal cord (cervical c-1)	Brain - Substantia nigra	Breast - Mammary Tissue	Cells - Cultured fibroblasts	Cells - EBV-transformed lymphocytes	Cervix - Ectocervix	Cervix - Endocervix	Colon - Sigmoid	Colon - Transverse	Esophagus - Gastroesophageal Junction	Esophagus - Mucosa	Esophagus - Muscularis	Fallopian Tube	Heart - Atrial Appendage	Heart - Left Ventricle	Kidney - Cortex	Liver	Lung	Minor Salivary Gland	Muscle - Skeletal	Nerve - Tibial	Ovary	Pancreas	Pituitary	Prostate	Skin - Not Sun Exposed (Suprapubic)	Skin - Sun Exposed (Lower leg)	Small Intestine - Terminal Ileum	Spleen	Stomach	Testis	Thyroid	Uterus	Vagina	Whole Blood
1	0.84968394	0.8573682	0.85443765	0.82785386	0.8405348	0.83592635	0.8288909	0.8614947	0.8621079	0.86819685	0.82743853	0.82081664	0.84860134	0.86256295	0.86479187	0.8665389	0.8512182	0.8712268	0.84598494	0.86883926	0.85942906	0.8509599	0.87322223	0.8492014	0.8481797	0.8562976	0.8675173	0.8551014	0.8384222	0.84500504	0.84326905	0.8584442	0.8759451	0.85840636	0.88302743	0.8497585	0.860178	0.8509782	0.86537397	0.84920055	0.8792636	0.87121475	0.8462427	0.8576953	0.8551431	0.87143594	0.8930454	0.8750065	0.84019804	0.87396765	0.83557403	0.84311163	0.87467927
2	0.83895123	0.8343612	0.8298761	0.82199395	0.82192963	0.7968263	0.8307266	0.81800175	0.8170125	0.8207113	0.723578	0.75132906	0.8097334	0.8212083	0.8253972	0.81627834	0.8182904	0.8213665	0.8375982	0.8165619	0.8544024	0.78678966	0.8148767	0.8300732	0.80908716	0.8347909	0.8299305	0.8374791	0.8354722	0.8295299	0.8236433	0.80426395	0.797258	0.8216505	0.83364785	0.83438474	0.85284644	0.79705846	0.82240963	0.798681	0.8464341	0.83809835	0.8383695	0.8355557	0.8354534	0.83957136	0.84319717	0.8381713	0.76055014	0.802122	0.8142478	0.84807587	0.8320872
3	0.94990903	0.9500262	0.96086276	0.9507657	0.9527458	0.95124644	0.956538	0.9448721	0.93556434	0.9404098	0.912032	0.91218966	0.929809	0.92930955	0.94656116	0.93947124	0.932442	0.945741	0.9508486	0.9490776	0.9514591	0.9571419	0.9537283	0.9566221	0.94590634	0.9568837	0.9533268	0.955526	0.95586807	0.9550718	0.93325883	0.94532585	0.9507025	0.9527365	0.9576734	0.9438642	0.95000553	0.9386064	0.9389464	0.94185716	0.9584864	0.9386424	0.9522991	0.9454492	0.9452857	0.9541873	0.9587205	0.95456374	0.91552055	0.9440998	0.94690955	0.9511154	0.9538746
4	0.66383517	0.65358347	0.6856481	0.68188876	0.6772169	0.66304415	0.6897646	0.6025648	0.6256563	0.63855565	0.6032933	0.6459148	0.65917224	0.6277319	0.623116	0.61480093	0.6043807	0.65707874	0.64441454	0.63375884	0.658697	0.64484483	0.6045522	0.6537133	0.6441805	0.7078532	0.67487085	0.7006858	0.67629486	0.7179468	0.63680744	0.6377591	0.6413164	0.6335269	0.61699945	0.64880025	0.69777286	0.6294916	0.68338287	0.6118497	0.6382142	0.6253558	0.64951193	0.6339547	0.6476022	0.6448241	0.70647943	0.6524449	0.59490335	0.63531137	0.6318237	0.66594946	0.6322639
5	0.94516075	0.9504159	0.9496317	0.9448451	0.95014036	0.9351665	0.9348823	0.9194937	0.9188514	0.9230591	0.83977205	0.8668829	0.91940343	0.92177355	0.9202	0.9276293	0.9137637	0.9250215	0.9198702	0.9329916	0.93696296	0.9471179	0.91952944	0.9185726	0.91343766	0.9394409	0.947162	0.9448663	0.9406872	0.94791496	0.9130702	0.9509269	0.9482428	0.934765	0.94196546	0.93576896	0.9514066	0.94778633	0.91164625	0.8987833	0.9390998	0.91655445	0.9258796	0.93320656	0.9360073	0.9392521	0.93816245	0.94464225	0.85342246	0.90863895	0.90582675	0.92608005	0.92377627
6	0.9512707	0.95454043	0.955742	0.9509466	0.95545834	0.9426406	0.9433716	0.9250286	0.9265804	0.9293979	0.8528031	0.87790966	0.92361087	0.9263843	0.9267666	0.9331527	0.9211604	0.93254805	0.9293966	0.9384743	0.94264615	0.95481694	0.925292	0.92770493	0.9228808	0.94696915	0.95198935	0.9503826	0.94648916	0.9534141	0.92455167	0.95611095	0.9542403	0.94148815	0.9469306	0.9420104	0.9563278	0.9498618	0.9207492	0.90948343	0.9452934	0.925645	0.9316037	0.93772334	0.94243985	0.9443485	0.9427036	0.95033395	0.8643495	0.9175434	0.91594344	0.93442565	0.9318248
7	0.86397296	0.86746615	0.88374984	0.8767478	0.8800268	0.8612379	0.86078864	0.8503564	0.8532217	0.8569271	0.77435577	0.8022825	0.85560477	0.84525603	0.8560278	0.8616382	0.8405423	0.8638078	0.8611984	0.86927205	0.86064005	0.87236387	0.8129018	0.8445736	0.83713543	0.8635236	0.88073844	0.88153136	0.8741933	0.8876031	0.8349956	0.8973886	0.88783914	0.8679245	0.85794497	0.8613699	0.89624107	0.850076	0.8459414	0.7855401	0.8736121	0.8407768	0.8603221	0.8601667	0.86669654	0.86505556	0.8640528	0.8815363	0.7505361	0.8320877	0.82098305	0.85576594	0.82720774
8	0.74600905	0.7238932	0.7774273	0.7792994	0.77127254	0.74941194	0.7751236	0.70033807	0.7066802	0.7126911	0.6447074	0.675048	0.730209	0.7073987	0.71250427	0.6978596	0.6819447	0.7322815	0.7178582	0.7223314	0.7292094	0.7310871	0.6801197	0.73729926	0.70769775	0.7742132	0.74761355	0.77408016	0.72798043	0.78077316	0.73620236	0.7321458	0.74658024	0.7271059	0.7168058	0.7074397	0.7709116	0.7320959	0.7459578	0.65664136	0.7347919	0.6684944	0.7229661	0.725994	0.73587835	0.71881735	0.74708545	0.751377	0.63139814	0.6988515	0.703585	0.7633378	0.729386
9	0.74709934	0.7418573	0.8106197	0.7279986	0.75908184	0.709865	0.7806756	0.72347385	0.7304086	0.7335598	0.7067414	0.70608795	0.71420336	0.7438307	0.7307808	0.7398007	0.7317089	0.73930156	0.7328101	0.74611413	0.75448495	0.7838267	0.744593	0.7389941	0.7466906	0.75573	0.79689443	0.73152053	0.78475714	0.73449975	0.7595314	0.7348433	0.7623285	0.7653218	0.76102483	0.7553394	0.7725123	0.77740395	0.7170223	0.73376197	0.7515925	0.75378954	0.7725164	0.7617408	0.7481345	0.79279804	0.8090898	0.75854266	0.7479905	0.7958192	0.74646676	0.75011843	0.7324474
10	0.7325169	0.7080504	0.78723705	0.6927866	0.724087	0.6823088	0.7636376	0.6804254	0.6891089	0.70683295	0.6857985	0.70097464	0.68910104	0.7083628	0.6907978	0.7107412	0.7060549	0.70051146	0.711305	0.7176836	0.7421918	0.7534275	0.69515276	0.7134668	0.7321815	0.72020954	0.7546852	0.7156718	0.7724274	0.7142967	0.7385094	0.71836025	0.7495484	0.73850644	0.72979474	0.73349315	0.76750165	0.7552899	0.7004414	0.6698346	0.7029677	0.7272819	0.7639408	0.74366987	0.72868013	0.75230205	0.78755987	0.7385495	0.7169949	0.7675293	0.69565934	0.74751043	0.62931293
11	0.91407156	0.91713667	0.9357424	0.92579997	0.9258052	0.9212577	0.90470296	0.92696273	0.9263951	0.9297387	0.8626903	0.8779972	0.9305943	0.9281372	0.9290339	0.9294899	0.9236824	0.9344307	0.92099607	0.9299323	0.90234864	0.9279354	0.91649914	0.8953023	0.89273006	0.9175817	0.92772734	0.915983	0.9243611	0.9166576	0.89455557	0.94264156	0.94332045	0.9375571	0.9367256	0.9062926	0.9281821	0.9438356	0.89163953	0.8972319	0.93262804	0.9177275	0.8921747	0.89624226	0.897985	0.92451537	0.92157686	0.9414336	0.8664072	0.89876115	0.88473684	0.8866402	0.91779196
12	0.82760143	0.83204937	0.8628601	0.85160285	0.8464257	0.8278438	0.80785626	0.84114134	0.8377935	0.85546494	0.7551175	0.79684144	0.84988487	0.84654456	0.8503391	0.8466544	0.8501183	0.8578949	0.82693005	0.8406556	0.8149306	0.8062314	0.803034	0.81452596	0.79407865	0.83320224	0.8511246	0.83432657	0.8460727	0.83332765	0.7987151	0.86772156	0.8646943	0.8662308	0.8568735	0.83144313	0.86123	0.8575916	0.80087644	0.7647201	0.8436778	0.8258563	0.8057254	0.7975041	0.7947777	0.83943	0.81594944	0.86224926	0.7273362	0.7880707	0.7760471	0.80509645	0.8172555
13	0.83343667	0.84021556	0.8740217	0.85634327	0.85351974	0.83678436	0.81808585	0.84820193	0.8443076	0.85778904	0.7790885	0.81153905	0.85909426	0.8536908	0.8534508	0.85632706	0.8535069	0.85966986	0.834246	0.8465274	0.8195283	0.8235539	0.818864	0.81656426	0.80857974	0.84475964	0.8580844	0.8466347	0.8570935	0.84520996	0.80956924	0.8723469	0.8734846	0.87273407	0.85818243	0.8417667	0.8688307	0.86123484	0.81050795	0.78973687	0.8487048	0.83948994	0.81372976	0.8112408	0.8109148	0.8496871	0.82846785	0.8692179	0.74443144	0.80300504	0.7866528	0.8022906	0.81492186
14	0.9073515	0.9103961	0.92607516	0.92117244	0.92160785	0.9155405	0.8985611	0.92246485	0.9224347	0.92599773	0.85449755	0.8697812	0.926483	0.924438	0.925282	0.9265674	0.9198723	0.9294472	0.9146288	0.92379105	0.8964437	0.92415774	0.9052393	0.89159214	0.8880688	0.9130802	0.91986674	0.9116934	0.9164133	0.9119917	0.88878953	0.9365697	0.93796223	0.9281284	0.9308816	0.9030093	0.920266	0.93733597	0.8863055	0.88585204	0.92646617	0.90966356	0.88793886	0.8884543	0.89060724	0.91642106	0.9109786	0.93313277	0.85545814	0.8938258	0.8803527	0.88123685	0.90915823
15	0.90923786	0.91065466	0.9265529	0.9207506	0.9204068	0.9182707	0.8988161	0.9234947	0.92260045	0.9265722	0.85485303	0.8721196	0.9287211	0.9261864	0.92614716	0.9278886	0.92017955	0.9299387	0.9168146	0.9256257	0.89779395	0.924808	0.9090807	0.89117205	0.8875772	0.91303426	0.9187926	0.912028	0.91752416	0.91270435	0.8879217	0.9372218	0.9386894	0.92829084	0.9292076	0.9023737	0.91949254	0.9395277	0.8863737	0.88572294	0.92507803	0.90831614	0.8898918	0.8887812	0.8905368	0.91579455	0.91033334	0.9329545	0.8580456	0.8908783	0.8798951	0.8810487	0.909427
16	0.8602273	0.8583001	0.8797926	0.86827964	0.8752721	0.86599255	0.84968436	0.8725716	0.8786241	0.87942964	0.76478237	0.8008796	0.8782212	0.8760465	0.87741363	0.8765494	0.8766171	0.88206637	0.853994	0.87459373	0.8399364	0.86656	0.84651196	0.80821973	0.80971134	0.858527	0.8739873	0.85354817	0.86425275	0.86125135	0.8247094	0.8734511	0.8829136	0.8647051	0.8752306	0.8534626	0.87700593	0.88156354	0.84580934	0.79319394	0.87750614	0.84769714	0.8395311	0.8277601	0.836119	0.87667716	0.8671384	0.88546866	0.784528	0.829875	0.8024996	0.8244095	0.84125817
17	0.89859694	0.89795923	0.916214	0.9094664	0.91197854	0.90983903	0.891013	0.91122496	0.9132098	0.91506803	0.84498703	0.85650903	0.9179428	0.9172953	0.9149941	0.9181547	0.9091576	0.91755295	0.9034201	0.9125822	0.88698924	0.91843903	0.8932158	0.88664496	0.8819984	0.9058201	0.9062309	0.90327185	0.90001327	0.90421325	0.88334846	0.9248203	0.92612106	0.9145051	0.92292196	0.89466774	0.90725935	0.92443764	0.8798872	0.87042445	0.9170413	0.9016773	0.8813025	0.87277937	0.87573355	0.9031371	0.8980996	0.9164313	0.84511757	0.8821065	0.876787	0.86872137	0.89067566
18	0.90128195	0.89974976	0.9163455	0.91082513	0.9127563	0.91407144	0.89269793	0.91504127	0.9162118	0.91808254	0.8474339	0.8613331	0.9217826	0.92023593	0.91771823	0.9215518	0.9122571	0.91954404	0.9087303	0.9170617	0.89009917	0.91764194	0.900092	0.8857821	0.882109	0.90713674	0.9053521	0.9043385	0.90478194	0.90636647	0.8830474	0.9269101	0.9268697	0.91549903	0.92217904	0.89549094	0.9060098	0.93030584	0.87867785	0.8724238	0.9143793	0.9006112	0.8822645	0.8755104	0.8772758	0.90311784	0.8970152	0.9184691	0.85019815	0.87986195	0.8777112	0.8713827	0.89186126
19	0.5148861	0.4838584	0.5241456	0.51845473	0.4904287	0.49661547	0.52218145	0.4668033	0.47564015	0.49286398	0.50819784	0.5628712	0.50135964	0.48381543	0.46464968	0.45198423	0.48767385	0.48941964	0.46439314	0.47637957	0.5003433	0.40299258	0.47041106	0.5115839	0.5068773	0.46910176	0.46826062	0.4578019	0.52419436	0.45541826	0.5266739	0.47750005	0.4974044	0.49718517	0.5065816	0.52356845	0.5070601	0.47708526	0.5373729	0.5202588	0.5242063	0.57200444	0.526701	0.49444056	0.4886077	0.5066331	0.5319418	0.51575613	0.4835156	0.55610806	0.4582719	0.48316178	0.44541487
20	0.83246815	0.8220504	0.85688514	0.84707963	0.85047656	0.82843083	0.82732993	0.81118757	0.8202332	0.82369053	0.76004976	0.80066645	0.8229685	0.8129635	0.8122606	0.8088685	0.81200254	0.82062566	0.8121486	0.8189365	0.82527226	0.80756533	0.8298448	0.83003634	0.8169193	0.8328595	0.8335435	0.84027576	0.8517395	0.8373976	0.81677246	0.81726485	0.83186454	0.8384017	0.82542115	0.834849	0.8543849	0.827336	0.8107222	0.8065051	0.8251623	0.841436	0.845122	0.8081605	0.82364637	0.8481552	0.84596634	0.8436537	0.7575201	0.83395845	0.8003419	0.83060914	0.81943476
21	0.93237484	0.93161935	0.94380283	0.9413832	0.93824065	0.9315014	0.94044226	0.9172242	0.91929924	0.9189434	0.87254846	0.88190764	0.90589523	0.90886575	0.9173559	0.9228865	0.9112426	0.922983	0.927125	0.9273774	0.9306048	0.93329716	0.93031776	0.9283554	0.9276662	0.9302908	0.9435089	0.937774	0.94533396	0.93875456	0.9251503	0.9335715	0.9375416	0.94229364	0.9340962	0.9353548	0.94764835	0.93291634	0.9243271	0.9136669	0.94678676	0.9223601	0.9407562	0.931266	0.9334772	0.9404181	0.9403165	0.94730675	0.8844078	0.9354614	0.91487855	0.9343748	0.927917
22	0.928537	0.9245998	0.9322461	0.9370645	0.9320175	0.9285679	0.94019425	0.901313	0.8954921	0.8992651	0.8702776	0.88328934	0.88265455	0.8904606	0.9014336	0.9048706	0.89053124	0.90569985	0.90964776	0.9148289	0.92297727	0.9302785	0.931296	0.9286455	0.9294113	0.9308885	0.94530755	0.93284166	0.93541497	0.9335186	0.91981345	0.924277	0.92908776	0.93391705	0.9265779	0.9276354	0.9493076	0.92359704	0.9220603	0.91484624	0.93902606	0.91986054	0.93058664	0.92746526	0.9281828	0.94167244	0.93956643	0.9404	0.88879144	0.93194485	0.9219629	0.93191546	0.924389
23	0.9283637	0.92405206	0.9320523	0.9371664	0.9317872	0.9290888	0.9400579	0.90054196	0.8947786	0.8988401	0.8704626	0.8830897	0.88172865	0.89016134	0.9010991	0.90402997	0.8902402	0.9051124	0.90958196	0.91440564	0.92319536	0.93074065	0.9319048	0.92853296	0.92977536	0.9308527	0.94520205	0.93295443	0.9347412	0.93338776	0.91996825	0.9237623	0.928755	0.93365943	0.9257433	0.9271186	0.9487368	0.92406005	0.9232441	0.91486055	0.9383974	0.9197427	0.93080837	0.9274827	0.92795163	0.9411294	0.93934214	0.93972206	0.88889253	0.9320772	0.9223173	0.9316037	0.9240077
24	0.9229984	0.9248651	0.9288824	0.93193805	0.92742187	0.92679006	0.93519706	0.8991693	0.8993284	0.9018758	0.8660077	0.8770809	0.8844	0.8912414	0.9014284	0.9037474	0.8908683	0.90938884	0.9121523	0.91397554	0.9193457	0.92428046	0.9218782	0.92255306	0.927071	0.9269155	0.94179046	0.93130624	0.934523	0.93172264	0.91473186	0.9251665	0.92952883	0.9331131	0.9258736	0.92415965	0.9457911	0.9279497	0.9217973	0.90905046	0.93912286	0.91771966	0.9265585	0.9234087	0.9245659	0.9403642	0.93894976	0.93924934	0.8757825	0.929661	0.9136151	0.92598534	0.9250633
25	0.926321	0.92526835	0.9279283	0.9353447	0.9316429	0.928747	0.94068575	0.9022722	0.900321	0.9038242	0.8701943	0.87931806	0.8850271	0.8891328	0.9046224	0.9064411	0.8924324	0.9097969	0.9139665	0.91717976	0.92256916	0.93007296	0.9246637	0.92655504	0.9299843	0.93003243	0.94267416	0.93301994	0.93625754	0.93347263	0.9201044	0.9240898	0.92949665	0.93412846	0.9263752	0.9264287	0.9463023	0.92760956	0.9229372	0.9135138	0.9407762	0.919462	0.9273659	0.9249004	0.9262619	0.9418845	0.94115144	0.93945295	0.8808873	0.93068266	0.9190588	0.92791873	0.9263468
26	0.92093784	0.9130548	0.9119048	0.92865163	0.9220151	0.91959846	0.9333476	0.8967762	0.8879358	0.8993397	0.8618177	0.874276	0.87191504	0.877127	0.8988155	0.89607847	0.8869227	0.90598613	0.91079676	0.91087186	0.9166958	0.9244316	0.9210121	0.9181078	0.9221287	0.9259672	0.9396801	0.9282443	0.92481375	0.92617273	0.90916187	0.91723526	0.92062485	0.92087764	0.91126204	0.91742027	0.9397605	0.9114583	0.91763246	0.8980342	0.93011653	0.90392935	0.91698706	0.9178637	0.9204372	0.93857783	0.9350878	0.9335062	0.880074	0.91502225	0.913771	0.92251456	0.91272783
27	0.9360441	0.93754387	0.9378196	0.93059856	0.93400544	0.92073405	0.93008024	0.90754044	0.90150464	0.9104866	0.85097444	0.8648588	0.88763	0.88124293	0.90646374	0.89415234	0.89694005	0.9190024	0.9111303	0.9124007	0.9342758	0.9157637	0.91229045	0.91819745	0.91974485	0.9281826	0.9429575	0.9354464	0.9459235	0.9353344	0.9228759	0.929505	0.9320841	0.94114816	0.93589705	0.93418884	0.94922334	0.9220665	0.9259375	0.91102326	0.9435218	0.9275807	0.9395231	0.9378897	0.94035035	0.94557846	0.9434717	0.95079076	0.86401594	0.943103	0.90950954	0.93546736	0.93597066
28	0.775777	0.78724563	0.8414637	0.7778126	0.79933417	0.7817564	0.8016636	0.8197063	0.8342703	0.8333728	0.7181636	0.73910725	0.8372518	0.8266317	0.83413374	0.82771146	0.82529974	0.832466	0.8104701	0.82174903	0.7843789	0.770418	0.762564	0.76538426	0.7512001	0.78398	0.8196338	0.8024616	0.82721615	0.8127287	0.7873874	0.8274334	0.8421814	0.8438142	0.83970296	0.76954013	0.81748027	0.8042429	0.7560166	0.6930539	0.8279761	0.7880165	0.7917965	0.8102954	0.8210645	0.7893211	0.7902684	0.8243229	0.72726405	0.7365767	0.7345691	0.7811078	0.7928408
29	0.7755911	0.78365535	0.7955662	0.7726702	0.78081405	0.7447791	0.76837456	0.76806813	0.7593347	0.78946817	0.71571994	0.7423885	0.75488675	0.76050484	0.7767417	0.75515807	0.7560926	0.79323375	0.7844582	0.7785039	0.76967335	0.7723901	0.6986845	0.73087585	0.7438265	0.77657557	0.81567764	0.7922081	0.8082425	0.81479293	0.78027135	0.77660686	0.792617	0.7959313	0.7931905	0.77055144	0.8104944	0.7810618	0.78024703	0.6806043	0.77464974	0.75711787	0.7836178	0.7490552	0.75727844	0.8089902	0.809889	0.7984759	0.70388234	0.7652801	0.73691046	0.7531263	0.7549575
30	0.86907303	0.87709534	0.8892682	0.87890136	0.8797976	0.8652977	0.86624134	0.8751129	0.8729046	0.8730911	0.7953715	0.8016896	0.86001766	0.8556253	0.87606984	0.8513564	0.8616775	0.87776357	0.8659916	0.8667097	0.85733044	0.8636133	0.86460906	0.84825706	0.86301917	0.87906754	0.9028522	0.8837965	0.90144175	0.890666	0.8819518	0.8645133	0.8685664	0.884997	0.86303884	0.8631667	0.8997812	0.8736907	0.8517563	0.82723045	0.8892733	0.848231	0.88322103	0.8802334	0.8852254	0.89971745	0.89269936	0.8960395	0.83525074	0.8867612	0.86124974	0.8613554	0.87867373
31	0.97092545	0.9738407	0.9726168	0.9705167	0.9719955	0.96529067	0.967004	0.97283256	0.96943796	0.9717625	0.9308685	0.937183	0.9692934	0.9647868	0.973098	0.97087	0.9663455	0.9743085	0.9705864	0.97507733	0.9705836	0.9678353	0.95958966	0.969169	0.9653621	0.96882117	0.97737944	0.97429246	0.9713813	0.97563934	0.96830285	0.97678024	0.9754341	0.97956944	0.98149365	0.96961844	0.97641927	0.97243583	0.9672562	0.9622671	0.98063356	0.96369827	0.9725809	0.9701904	0.9697736	0.9755146	0.9726264	0.9798109	0.9435636	0.96781576	0.9630855	0.9674386	0.97016114
32	0.9809187	0.98109424	0.98273295	0.9826487	0.98353195	0.978567	0.9761998	0.97807217	0.97395384	0.97686213	0.9439065	0.9506919	0.9697952	0.96719944	0.9782325	0.9739771	0.97268903	0.9795052	0.9789502	0.97876567	0.9817687	0.98147506	0.97299594	0.9791468	0.9767038	0.98164785	0.9834835	0.98407555	0.98510504	0.9855609	0.9778174	0.98395765	0.98436326	0.9828917	0.9856383	0.9801574	0.9837014	0.9831983	0.9754168	0.9763497	0.9868142	0.97566974	0.97952974	0.98152065	0.98201495	0.98002803	0.98117673	0.9851729	0.95371073	0.9772339	0.9751421	0.9780224	0.9816267
33	0.9817122	0.98215216	0.98367465	0.9831109	0.9838104	0.97890437	0.9771002	0.9806876	0.9764554	0.9787552	0.9427277	0.9489355	0.9730997	0.97066057	0.98043	0.97687304	0.9751271	0.9816497	0.98083484	0.9812145	0.9823661	0.9819382	0.9727868	0.9791126	0.97674626	0.9827916	0.98450166	0.9845502	0.98600876	0.9856249	0.9768685	0.9847182	0.9854747	0.98561704	0.98682106	0.98074085	0.9854784	0.98394763	0.9750999	0.97697955	0.98784864	0.9763883	0.9809701	0.9825989	0.9831155	0.9813431	0.9823836	0.9866927	0.9544281	0.97746074	0.9751999	0.97978556	0.9834778
34	0.90410125	0.90680903	0.92128646	0.9143958	0.9158481	0.8918082	0.8997816	0.92019033	0.9175846	0.9191364	0.8220949	0.8395492	0.9100908	0.9162499	0.91915	0.9249789	0.91704196	0.9196264	0.9270242	0.9284948	0.90855324	0.9115389	0.85471135	0.8958686	0.8965312	0.91096485	0.92774934	0.90534735	0.9221341	0.9090401	0.8941072	0.9274341	0.92812806	0.92374074	0.9201213	0.8910345	0.9225856	0.9322237	0.9016053	0.8857511	0.92636603	0.8806467	0.8879943	0.9083681	0.91117775	0.9204297	0.9237857	0.92766094	0.8438548	0.8981447	0.88393563	0.9071585	0.89974517
35	0.9304651	0.9360754	0.9373642	0.9378651	0.9399136	0.91301155	0.9241265	0.9416006	0.9379646	0.9405562	0.84415454	0.86180687	0.9340555	0.93504936	0.93873155	0.94054794	0.9390136	0.9413017	0.9458993	0.9490113	0.93361175	0.9318949	0.887578	0.9217321	0.92073584	0.93365145	0.9469075	0.9325186	0.943766	0.9310853	0.9221939	0.94243354	0.9405548	0.9440449	0.9430636	0.9187519	0.9380477	0.9493167	0.9269924	0.9058603	0.9413884	0.90062684	0.9228462	0.9262284	0.9300885	0.9420837	0.94374263	0.9459003	0.8462122	0.92697465	0.91107005	0.92900574	0.9222956
36	0.37276235	0.38472813	0.44760126	0.372362	0.38463253	0.36715278	0.41816115	0.3950319	0.42877498	0.42786813	0.45232335	0.4676345	0.455053	0.4421401	0.40422136	0.41810757	0.42532867	0.42556134	0.41921002	0.41067284	0.37895823	0.35006508	0.3288232	0.40037045	0.40899235	0.36357552	0.38310692	0.36846977	0.43599766	0.36855298	0.40057832	0.37671006	0.4072884	0.38091877	0.4095339	0.40090442	0.38924876	0.45389405	0.40337506	0.38338327	0.42574772	0.44194323	0.40642586	0.43526858	0.44279003	0.3890094	0.4387764	0.40467644	0.40713868	0.37914062	0.36626363	0.41394567	0.4068156
37	0.40191346	0.40634757	0.44615278	0.39705473	0.4092539	0.4044037	0.43552646	0.42489815	0.45685062	0.45217052	0.41091973	0.42020637	0.46475536	0.46956053	0.43186265	0.4662307	0.4618371	0.45404863	0.41826898	0.43780708	0.40042695	0.3546711	0.3965548	0.40292516	0.40608087	0.41005453	0.40883064	0.39074016	0.40505153	0.38369936	0.4026986	0.42218208	0.47533503	0.4188973	0.45330304	0.4102736	0.4197692	0.46742886	0.3854998	0.3606917	0.46222892	0.42464933	0.42086166	0.42368037	0.422007	0.42772847	0.44507942	0.43524036	0.43923074	0.39076346	0.3789634	0.39115542	0.45674348
38	0.4691376	0.4679319	0.50362694	0.47989312	0.49773568	0.461327	0.50234014	0.46101514	0.46848312	0.48544127	0.48462301	0.48663735	0.47539192	0.4801535	0.46579772	0.4721485	0.47672677	0.493955	0.49828824	0.476755	0.4638551	0.40302858	0.39435464	0.48433357	0.4921872	0.47265634	0.48374778	0.45667648	0.50758064	0.46194023	0.48125058	0.4688631	0.49279913	0.475803	0.5026374	0.4970335	0.50455296	0.49088073	0.4750162	0.45198908	0.532062	0.49467832	0.48948687	0.5120142	0.5187799	0.4955965	0.5278772	0.51299065	0.46633315	0.4638737	0.45721117	0.47595787	0.5179861
39	0.45469823	0.43628588	0.47376496	0.4331115	0.45563206	0.4266189	0.48917022	0.4123408	0.4388849	0.430713	0.477571	0.5136075	0.46588764	0.47805786	0.41425338	0.4249959	0.43607974	0.4300545	0.4285265	0.41880354	0.45265284	0.42361134	0.4080407	0.44041795	0.45451146	0.4655818	0.48498982	0.45182982	0.50939286	0.45392948	0.44727486	0.4284223	0.4554248	0.43139118	0.49287686	0.4588147	0.48043832	0.45319575	0.4829255	0.45853528	0.5024455	0.48712936	0.47057968	0.49425825	0.50995857	0.4897833	0.49672437	0.47205067	0.4887423	0.48481122	0.45244223	0.46911916	0.4672882

Detailed arguments:

usage: iDARTS [-h] [--version]
              {get_resources,parse_vcf,build_feature,predict} ...

iDARTS - individualized Deep-learning Analysis of RNA Transcript Splicing

positional arguments:
  {get_resources,parse_vcf,build_feature,predict}
    get_resources       iDARTS get_resources: download hg19 fasta and
                        phastCons scores

    parse_vcf           iDARTS parse_vcf: get the predicted PSI values of
                        reference and alternative alleles as well as the
                        predicted deltaPSI in GTEx tissues or user-provided
                        RBP expression levels from the pre-compiled
                        alternative splicing events or user-provided events

    build_feature       iDARTS build_feature: build cis-sequence features for
                        alternative splicing events

    predict             iDARTS predict: predict PSI values given alternative
                        splicing events with annotated cis-sequence features
                        and RBP expression levels from the GTEx or user-
                        provided RBP expression levels

get_resources
  usage: iDARTS get_resources [-h] [-o OUT_DIR] [-f {True,False}]

  optional arguments:
    -h, --help            show this help message and exit
    -o OUT_DIR, --out-dir OUT_DIR
                          Optional, default user home directory: Output folder
                          for downloaded data
    -f {True,False}, --force {True,False}
                          Optional, force redownload of resources

parse_vcf
  usage: iDARTS parse_vcf [-h] [-t {SE,A5SS,A3SS}] [-i INPUT] -v VCF_PATH
                          [-e EXPR] -o OUTFILENAMEPREFIX  

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative 3
                          splice sites, A5SS: alternative 5 splice sites
    -i INPUT, --input INPUT
                          Optional, a list of alternative splicing events; If
                          not provided, the alternative splicing events will be
                          the pre-compiled events from GENCODEv26lift37
    -v VCF_PATH, --vcf_path VCF_PATH
                          the file location of the VCF
    -e EXPR, --expression EXPR
                          Optional, a list of RBP expression levels (TPM values
                          from Kallisto); header format
                          'Gene_ID\tExp1,Exp2,Exp3...(different expression
                          profiles separated by comma). If not provided, the
                          pre-compiled RBP expression levels from the GTEx will
                          be used.'
    -o OUTFILENAMEPREFIX, --outFileNamePrefix OUTFILENAMEPREFIX
                          output files name prefix (including full or relative
                          path).

build_feature
  usage: iDARTS build_feature [-h] [-t {SE,A5SS,A3SS}] -i INPUT
                              [-m {True,False}] -o OUTPUT

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative
                          3-prime splice sites, A5SS: alternative 5-prime splice
                          sites
    -i INPUT, --input INPUT
                          A list of alternative splicing events
    -m {True,False}, --mutate {True,False}
                          Whether annotate the sequence features with SNV (300nt
                          in the vicinity of skipped exons);
    -o OUTPUT, --out-file-name OUTPUT
                          Annotation output file name

predict
  usage: iDARTS predict [-h] [-t {SE,A5SS,A3SS}] -i INPUT [-e EXPR] -o OUTPUT

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative 3
                          splice sites, A5SS: alternative 5 splice sites
    -i INPUT, --input INPUT
                          A list of alternative splicing events with built cis-
                          sequence features; the input is the output of the
                          build_feature step
    -e EXPR, --expression EXPR
                          Optional, a list of RBP expression levels (TPM values
                          from Kallisto); header format
                          'Gene_ID\tExp1,Exp2,Exp3...(different expression
                          profiles separated by comma). If not provided, the
                          pre-compiled RBP expression levels from the GTEx will
                          be used.'
    -o OUTPUT, --out-file-name OUTPUT
                          The predicted PSI values for the alternative splicing
                          events

Contact

Mailing List / Group

GitHub Issues

Zhicheng Pan [email protected]

Yi Xing [email protected]

Copyright and License Information

Authors: Zhicheng Pan and Yi Xing

This program is licensed with commercial restriction use license. Please see the attached LICENSE file for details.

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iDARTS: individualized Deep-learning Analysis of RNA Transcript Splicing

Table of Contents

Installation

Usage

Predicting effects of variants on splicing

Input:

Output:

Example

Example 1:

Input: User-provided VCF file

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing

Example 2:

Input: User-provided VCF file and AS events

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events

Example 3:

Input: User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events and RBP expression levels

Output (Example1, Example2, and Example3):

Predicting splicing levels of AS events

Output format:

Detailed arguments:

Contact

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Name		Name	Last commit message	Last commit date
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bin		bin
example		example
iDARTS		iDARTS
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
requirements.txt		requirements.txt

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Xinglab/iDARTS

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iDARTS: individualized Deep-learning Analysis of RNA Transcript Splicing

Table of Contents

Installation

Usage

Predicting effects of variants on splicing

Input:

Output:

Example

Example 1:

Input: User-provided VCF file

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing

Example 2:

Input: User-provided VCF file and AS events

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events

Example 3:

Input: User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events and RBP expression levels

Output (Example1, Example2, and Example3):

Predicting splicing levels of AS events

Output format:

Detailed arguments:

Contact

Copyright and License Information

About

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