Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v


Sign In or Register to comment.