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.

A few things need help about output of command ModelSegments.

Hello, gatk team thanks for your good tools. Here I have some questions about output of ModelSegments.
1. *.cr.seg file NUM_POINTS_COPY_RATIO field. It's this the same with Num_Probes in CGH result? Or this means how many bins supporting this segment? I want to plot heatmap for multiple samples result use "copynumber" package in R.
2. *.igv.seg file last field Segment_Mean is absolute value of copy number ratio(all positive number in my case.)? It seems igv accept this field as log2 ratio.
3. *.modelFinal.seg LOG2_COPY_RATIO_POSTERIOR_(10/50/90) what's those posterior(10/50/90) meaning?

Best Answer


Sign In or Register to comment.