Commands to manipulate VCF files

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Authors	Christine Tranchant-Dubreuil
Research Unit	UMR DIADE
Institut

Description

This page describes some tools to manipulate and to extract easily informations from vcf file. We need, in this tutorial:

• a vcf file
• a reference file used for the mapping step.

Keywords : gatk,bcftools

Files format : vcf

Date : 10/03/2017

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Summary

• Extracting list of samples from a vcf file with grepand cutcommands
• Extracting a subset of samples from a multigenome vcf file with GATK selectVariants
• Extracting a subset of samples from a multigenome vcf file with bcftools
• Calculating the nucleotide diversity from a vcf file with vcftools

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Extracting list of samples from a vcf file with grepand cutcommands

one line with all samples

grep "#CHROM" output | cut -f 10- 

one line by sample

grep "#CHROM" output | cut -f 10- | xargs -n 1

Extracting a subset of samples from a multigenome vcf file with GATK selectVariants

Select two samples out of a vcf with many samples

java -Xmx12g -jar /usr/local/gatk-3.6/GenomeAnalysisTK.jar -T SelectVariants -R reference.fa -V inputFileName.vcf -o outputFilename.vcf -sn sample1 -sn sample2

Rk : if you get the following error message "Fasta dict file ... for reference ... does not exist", please see https://www.broadinstitute.org/gatk/guide/article?id=1601 for help creating in.

Select genotypes from a file containing a list of samples to include

java -Xmx12g -jar /usr/local/gatk-3.6/GenomeAnalysisTK.jar -T SelectVariants -R reference.fa -V inputFileName.vcf -o outputFileName.vcf --sample_file barthii.only.RG.list  --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES

Select genotypes from a file containing a list of samples to exclude

java -Xmx12g -jar /usr/local/gatk-3.6/GenomeAnalysisTK.jar -T SelectVariants -R reference.fa -V inputFileName.vcf -o outputFileName.vcf --exclude_sample_file barthii.only.RG.list  --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES

Rk : if you get the following error message : "Bad input: Samples entered on command line (through -sf or -sn)) that are not present in the VCF", run with --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES

Extracting a subset of samples from a multigenome vcf file with bcftools

Select genotypes from a file containing a list of samples to include with bcftools

bcftools view -S barthii.only.RG.list inputFileName.vcf --force-samples -o outputFilename.vcf`

Calculating the nucleotide diversity from a vcf file with vcftools

vcftools --vcf inputFilename.vcf  --out outputFilename.PI  --window-pi 100000 --remove-filtered-all

grep "PI" OgOb-all-MSU7-CHR2.GATKSV.VCFTOOLS.stats-100000.windowed.pi -v | awk '{ sum+=$5; print $5,"; ",sum , "* ", NR ; } END { print "PI average :", sum / NR; }'