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
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