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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
NCBI chr reference name different from dbSNP chr names, is that usable by GATK?
I am trying to perform base recalibration on a non-human genome. I've downloaded the dbSNP vcf file from Ensembl (also downloaded another version from NCBI), and for both files the chr naming system is "1, 2, 3...". On the other hand, the NCBI reference file I used named chromosomes differently, chr 1 = gi|966749131|ref|NC_006088.4|, chr2 = gi|966749130|ref|NC_006089.4|...
However, BaseRecalibration seemed to run fine. I am wondering if GATK is capable of internally recognizing the NCBI chromosome names or if their algorithm generated a completely wrong recal table and recalibrated all the scores wrong. I've also attached an output of my AnalyzeCovariates plot in case that helps. Thanks!