Consensus VCF file from several variant callers

Question

[ajuiwl]

Hi all, I want to do a consensus VCF file with only the variants that have been called by two variant callers. The problem is that for the same variant the INFO and FORMAT columns of the VCF files show different values, this is to say: GATK shows the variant with DP, MQ, FS values that differ from those shown by Freebayes. I understand that the programs have different internal parameters. But in order to obtain a single VCF file with just one value per each property (DP, MQ, FS etc...) what should I do?

I have checked the GIAB consensus vcf file and they just show one value per each property despite the fact that they have use several variant callers, but I have not found the method that they followed in order to merge that.

I would be very thankful if somebody could help in this issue.

Answer 1

[Pierre Lindenbaum]

GATK SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

with

 --concordance Freebayes.vcf  

A site is considered concordant if (1) we are not looking for specific samples and there is a variant called in both the variant and concordance tracks or (2) every sample present in the variant track is present in the concordance track and they have the sample genotype call.