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.
Can I use GISTIC2 for CNV data from targeted sequencing?
I have targeted panel sequencing data. The panel size is 1.2 Mbp with 33,524 probes targeting a total of 382 genes, including entire exons of 199 genes.
I got segmented log2 ratios and SEG files using CNVkit from this targeted bam files. I would like to check driver events using GISTIC2.
length-based filtering of arm-level events greatly improves the sensitivity of GISTIC. But my data is targeted, so I worry that the algorithm will work. Can I use CNV data from targeted sequencing instead of whole exome sequencing or whole genome sequencing as an GISTIC2 input?