Combine VCF files with multiple alternative alleles in GATK
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4.4 years ago
ciemanek ▴ 140

Hi all!

I am calling variants with 3 different tools and later on I'd like to make an intersection of resulting VCF files to make sure that my variants are reliable. I wanted to use GATK to combine variants from 3 methods but I wonder, how does it decide which variants are in common? Does it return only those variants with identical chromosome, position, reference and alternative allele? Or is it possible to somehow integrate the information from all samples and annotating variant to store the information about alternative alleles in particular samples? Or maybe in context of variants calling I should rely only on those records that called identical alternative alleles? What is the point of my analysis is to compare resulting sets to identify common and unique variants between control and impacted samples if that gives you any more context.

Any hint will be appreciated, Agata

gatk combine ngs sequencing variants calling • 1.5k views

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