Notice:
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.

Somatic-SNVs-Indels-GATK4 "workspace.intervals" file

Hi! We have WES samples that were analyzed using the Illumina exome capture kit. I have an intervals file (whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list) which I uploaded into the google bucket for my Somatic-SNVs-Indels-GATK4 workspace. I'm running the Mutect2 workflow, and out of curiosity I launched an analysis on one of my sample pairs in which I 1) designated my Illumina intervals file google bucket link as the attribute for the intervals file in the method config, and 2) where I filled in the "workspace.intervals" attribute for the intervals file variable. I kept everything else the same.

The results in the final MAF are similar but noticeably different when I use my Illumina intervals list vs. the workspace intervals file. I was just wondering what the workspace intervals file corresponds to? Is it meant Illumina or Agilent samples?

Thanks!

Answers

Sign In or Register to comment.