SNPextractor

Simple extractor script to extract list of SNPs from HRC VCFs for CBMR.

##Requirement

• Software/build upon:
• bcftools 1.3.1
• R 3.0.1
• python 2.7.3
• For users of CBMR porus cluster: You migth want to update your path to have the same programs as me, so edit your .bashrc file by:
• nano ~/.bashrc
• add export PATH=$PATH:/home/fng514/bin:/home/cxt155/bin:/home/cxt155/samtools-bcftools-htslib-1.0_x64-linux

Data

• Imputed dataset on HRC panel (2016), in .vcf format, split into chromosomes and tabix'ed
• List of SNPs with chromosome and position on build 37 (same as HRC panel). One SNP pr. line in the following order: SNPID chromosome positions
• Try using an online tool, such as: http://db.systemsbiology.net/kaviar/
• List of indidviduals as particids. One individual pr. line.

##How to install clone this repository with: git clone https://github.com/vincentrose88/SNPextractor.git

which will create the folder SNPextractor from where you will need to go to (cd SNPextractor) to run the program.

##How to use

Examples

Extract dosage information for 4 SNPs for three inter99 individuals from Decode dataset: ./extractor.sh -s SNPlist.example -i individualslist.example -v /emc/cbmr/data/imputed/decode-Nov09-sanger-hwe10e5/ -t DOSAGE -o inter99.decode.example -a

Extract genotype information for 4 SNPs for all individuals in studies 1 and 2 from Decode dataset: ./extractor.sh -s SNPlist.example -c 1,2 -v /emc/cbmr/data/imputed/decode-Nov09-sanger-hwe10e5/ -t GENOTYPE -o project.1.2.decode.example -a

Extract likelihood information for 4 SNPs for all individuals from decode dataset for an GRS: ./extractor.sh -s SNPlist.example -v /emc/cbmr/data/imputed/decode-Nov09-sanger-hwe10e5/ -t LIKELIHOOD -o all.decode.example -a -g

Run

Run the extractor.sh script with the following flags and arguments:

• -s (SNP): File containing the list of SNPs that needs to extracted with the following requirement:
• Each line has variant name, chromosome and position, seperated by '\t' (tab) or space ' ' (see example file).
• NB: Must be on same build as imputed data (commonly b37, but do check).
• -v (VCF): Path to vcf containing the HRC imputed data.
• For example: /emc/cbmr/data/imputed/decode-Nov09-sanger-hwe10e5/
• Only one link is allowed. For multiple datasources, clone this rep. multiple times.
• -t (type): Specify which type of data for each SNP is needed. Only one is allowed.
• Options are: DOSAGE, GENOTYPE or LIKELIHOOD. Default: DOSAGE
• -i (individuals): File containing a list of individuals you want extracted. One individuals particid on each line, using "\n".
• Optional parameters
• -o output filename. The suffix .csv will be added regardless. Default is: SNPsExtracted.csv. NB: Outputfiles with identical names will be overwritten
• -d date flag. Doesn't need an argument Use if you want to avoid having timestamp-names on the temporary work-directory. FORBIDDEN if you are using the same folder to extract several SNPs because of overwriting risk.
• -m memory requested post chromosomes extraction. How much memory do you want to request from the cluters grid engine after extracting from chromosomes? Default: 2G
• -c cohort's study-id. Specify the study-id to extract all individuals from that study. Multiple studyids allowed when seperated with ',' and no spaces, ie. 1,2,3.
• -a sanger server? Doesn't need an argument Is the imputation from the sanger server then add this flag. Default is the Micigan server (ie. do not add this flag, if the imputation is on the michigan server).
• -g GRS out put: Doesn't need an argument Output genoFile.nohead, newHeader and all.SNPs.vcf instead of standard csv-files, to be used directly in the GRS (move the .vcf file to the GRS/geno folder, and the other two to the GRS folder). Only works with DOSAGE (automatical sat)

Output

The extractions output is saved as two .csv files, one with only the genotype data (rows are individuals, columns are SNPs) and one with the info for each SNP (chromosome, position, ref and alt alleles).