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.

Converting ModelSegments outputs for ABSOLUTE


I work on exome data to detect somatic variants. I identified the SNPs/Indels with Mutect2 and I followed the ModelSegments tutorial to detect CNAs. Now I want to convert the AF outputs I got with ModelSegments into AllelicCapSeg outputs to use them with ABSOLUTE.

For this purpose, I tried to use part of this pipeline on GitHub (unsupported/combine_tracks_postprocessing_cnv/combine_tracks.wdl) to convert the data with the function "convert_model_segments_to_alleliccapseg". I use as input files from ModelSegments.

However, I don't really understand in the script the utility of the following parameters to use as threshold values (Float ? maf90_threshold and Int ? min_hets_acs_results)?

Is there a better way to do this conversion?

Thank you

Best Answer


  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 1

    Hi @Lea_F ,

    This is one of the few workflows in the GATK repo we do not support. We can help you with questions on workflows outside of the "unsupported" directory.

Sign In or Register to comment.