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nf-100GMX-variant-summarizer

Nextflow pipeline used to count variants for the 100GMX project

=== 'nf-100GMX-variant-summarizer' is a pipeline tool that counts variants in a VEPextended annotated VCF file. This pipeline generates 3 outputs: 1) a tsv file with the total number of SNV and indels; 2) a tsv file with per sample counts for variants of type SNV, indel, novel, worldwide singletons, clinvar, gwascat and pharmgkb; 3) a pdf file with the number of discernible variants in sample groups of interest.

Important note: input file must be previously annotated by https://github.com/Iaguilaror/nf-VEPextended

Features

-v 0.0.1

  • Supports vcf compressed files as input.
  • VCF input must be previously annotated by https://github.com/Iaguilaror/nf-VEPextended
  • Results include a tsv with total SNV and indels
  • Results include a tsv with per sample counts
  • Results include a pdf with number of discernible variants in sample groups
  • Scalability and reproducibility via a Nextflow-based framework.

Requirements

Compatible OS*:

* nf-100GMX-variant-summarizer may run in other UNIX based OS and versions, but testing is required.

Software:

Requirement Version Required Commands *
bcftools 1.9-220-gc65ba41 bcftools
htslib 1.9 tabix, bgzip
filter_vep 96 & 97 vep
Nextflow 19.04.1.5072 nextflow
Plan9 port Latest (as of 10/01/2019 ) mk **
R 3.4.4 Rscript

* These commands must be accessible from your $PATH (i.e. you should be able to invoke them from your command line).

** Plan9 port builds many binaries, but you ONLY need the mk utility to be accessible from your command line.

Installation

Download nf-100GMX-variant-summarizer from Github repository:

git clone https://github.com/Iaguilaror/nf-100GMX-variant-summarizer

Test

To test nf-100GMX-variant-summarizer's execution using test data, run:

./runtest.sh

Your console should print the Nextflow log for the run, once every process has been submitted, the following message will appear:

======
VCF summarizer: Basic pipeline TEST SUCCESSFUL
======

nf-100GMX-variant-summarizer results for test data should be in the following file:

nf-100GMX-variant-summarizer/test/results/VCFsummarizer-results

Usage

To run nf-100GMX-variant-summarizer go to the pipeline directory and execute:

nextflow run summarize-vcf.nf --vcffile <path to input 1> --metadata <path to input 2> --nsamples <integer> --group_minaf <numeric> --outgroup_maxaf <numeric> [--output_dir path to results ]

For information about options and parameters, run:

nextflow run summarize-vcf.nf --help

Pipeline Inputs

Example line(s):

##fileformat=VCFv4.2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr21	5101724	.	G	A	.	PASS	AC=1;AF=0.00641;AN=152;DP=903;ANN=A|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19987C>T|||||||||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5101724G>A||||||||||||||||||||||||||||2.079|0.034663||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
chr21	5102165	rs1373489291	G	T	.	PASS	AC=1;AF=0.00641;AN=140;DP=853;ANN=T|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19546C>A|||||||rs1373489291||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5102165G>T||||||||||||||||||||||||||||5.009|0.275409||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  • *.tsv : A metadata file, relating every sample ID (as registered in the VCF file) and a sample group in column format.

Example line(s):

sample	group
SM-3MG5L	Chinanteco
SM-3MG5F	Chocholteco
SM-3MG46	Kanjobal

Pipeline Results

  • A tsv file with *.total_variants.tsv extension.

Example line(s):

# Variants in project sample.vcf.gz
number of SNPs: 8769
number of indels:       1231
  • A tsv file with *.persample_counts.tsv extension.

Example line(s):

sample SNV indel total_variants tstv_ratio missing_sites heterozygosity_ratio novel_total_variants worldwide_singletons clinvar_pato_likelypato_and_riskfactor_variants variants_in_gwascat variants_in_pgkb
SM-3MG3L 3183 444 3627 2.196 4 1.091 1 10 0 6 0
SM-3MG3M 3100 450 3550 2.173 1 1.115 1 13 0 5 0
  • a tsv file named private_variants_per_group.tsv

Example line(s):

group variant_type number
Nahua snv 0
Nahua indel 0
Seri snv 2
Seri indel 0

References

Under the hood nf-100GMX-variant-summarizer uses some coding tools, please include the following ciations in your work:

  • McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R., Thormann, A., ... & Cunningham, F. (2016). The ensembl variant effect predictor. Genome biology, 17(1), 122.
  • Narasimhan, V., Danecek, P., Scally, A., Xue, Y., Tyler-Smith, C., & Durbin, R. (2016). BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics, 32(11), 1749-1751.
  • Team, R. C. (2017). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http s. www. R-proje ct. org.

Contact

If you have questions, requests, or bugs to report, please email [email protected]

Dev Team

Israel Aguilar-Ordonez [email protected]

Cite us

If you find this pipeline useful for your project, please cite us as:

Aguilar-Ordoñez, Israel, et al. "Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights." PloS one 16.4 (2021): e0249773.