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Old 10-10-2014, 02:29 PM   #1
ronton
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Location: US

Join Date: Jun 2014
Posts: 34
Default How to view only the variants that are present in multiple VCF files?

Suppose I have 10 .vcf files and I want to generate a .vcf file that only contains the common variants that are present in all of the 10 files. Can I use GATK CombineVariants followed by SelectVariants intersection to achieve this? Is there another way?

Thank you

"If you want to extract just the records in common between two VCFs, you would first run CombineVariants on the two files to generate a single VCF and then run SelectVariants to extract the common records with -select 'set == "Intersection"', as worked out in the detailed example in the documentation guide."

https://www.broadinstitute.org/gatk/...neVariants.php
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