Filter all the common SNP's in different vcf files(corresponding to different samples)

Question

[shubhra.bhattacharya]

I have 10 different vcf files which are of different samples.

I want to find the SNPs common between all of them i.e the snp should be present in all the 10 samples.

For that I am using vcftools isec but I am getting 10 different files instead of one single file with the common snps.

The readme file says: 0000.vcf has stripped reads for sample 1 , 0001.vcf has stripped reads for sample 2 and so on.

The command used is:

/data/ngs/programs/bcftools-1.3/bcftools isec -p match/ -n=10 qual-out-1.vcf.recode.vcf.gz qual-out-2.vcf.recode.vcf.gz ... qual-out-10.recode.vcf.gz

I have obtained these files from GATK pipeline.My ultimate aim is to just get one single vcf with all common snps

[sacha]

bedtools intersect -a file1.vcf -b file2.vcf file3.vcf file4.vcf

Or alternative software:

• snpSift intersect http://snpeff.sourceforge.net/SnpSift.html#intersect

• variant tools http://varianttools.sourceforge.net/Vtools/Compare

Answer 1

[Pierre Lindenbaum]

merge your files with gatk combinevariants. https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

then use https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php with --maxNOCALLnumber 0

[shubhra.bhattacharya]

Due to some technical difficulties I am unable to use GATK and hence I am forced to use other options.

Answer 2

[cpad0112]

try bcftools concat with -d option