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.
Quality recalibration with the latest GATK jar (GenomeAnalysisTK-2.1-9-gb90951c)
I have been using GATK for realignment and recalibration steps on mapped BAM file before we call SNP calling. I just downloaded the latest GATK jar (GenomeAnalysisTK-2.1-9-gb90951c) and started testing these walkers.
With the earlier version of GATK, I was calling CountCovariates followed by TableRecalibration as a part of Quality score recalibration.
Essentially CountCovariates and TableRecalibration options are not available in the latest GATK jar. I would like to know the equivalent steps.
I suspect with the latest GATK version, both these steps has been merged as BaseRecalibrator?? But the output from BaseRecalibrator is recal_data.grp. Can anyone explain about Quality score recalibration step in the latest GATK version. Thanks.