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.
Hi, I met a problem when I try to use genotype concordance to compare one trio tested on 2 different platform. One is Agilent, the other is Nimblegene. I want to compare the concondance of each family members in the 2 platforms. I got the following:"1305446EX.combined.vcf and reference have incompatible contigs: No overlapping contigs found" I am use hg19.fasta as reference
I guess my method using concondance might be not 100% correct or something I misunderstood. Could you guide me how to compare them?