Finding common variants in multiple VCF files

Question

[priyanka16161]

Hi,

I am having 54 vcf files of same study. In this I have to separate common and unique variants and for common variants, I need to calculate allele frequency. VCF files are generated by GATK.

Thanks
Priyanka

Answer 1

[igor]

GATK includes a tool CombineVariants to combine VCFs.

CombineVariants reads in variants records from separate ROD (Reference-Ordered Data) sources and combines them into a single VCF. Any number of sources can be input. This tool aims to fulfill two main possible use cases, reflected by the two combination options (MERGE and UNION), for merging records at the variant level (the first 8 fields of the VCF) or at the genotype level (the rest).

Full docs here: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php