Merge VCF with 1000 Genome Phase 3 VCF

bassubassu UAEMember
edited December 2017 in Ask the GATK team

Hi,

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: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v
5a.20130502.genotypes.vcf.gz

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