Question: Finding common variants in multiple VCF files
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gravatar for priyanka16161
3.0 years ago by
priyanka161610 wrote:

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

Thanks Priyanka

snp next-gen forum • 2.7k views
ADD COMMENTlink modified 3.0 years ago by igor7.4k • written 3.0 years ago by priyanka161610
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gravatar for igor
3.0 years ago by
igor7.4k
United States
igor7.4k wrote:

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

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by igor7.4k
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