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Merge VCF with 1000 Genome Phase 3 VCF

bassubassu UAEMember
edited December 2017 in Ask the GATK team


I would like to merge my vcf with 1000 Genome Phase3 vcf. The issue for me is difference in chromosome position for the same data

eg: RSID rs112185012 in my vcf is at "1:972645" and in 1000 Genome Phase3 its at "1: 908025"

Source for 1000 Genome VCF:


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