If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

Start to use GISTIC2


I have called somatic copy number in tumor-matched normal by scatngs

I have 3 output files, this is one output of scatngs

Chromosome Position Log R segmented LogR BAF segmented BAF Copy number Minor allele Raw copy number
rs62635286 1 13116 -1.23040761342626 0.00160351549950095 0 0.317683333333333 2 1 0.41361756890851
rs75454623 1 14930 -0.390888460751959 0.00160351549950095 0.3548 0.317683333333333 2 1 1.19149081633643

Could you please tell me which columns corresponds to

Num markers (number of markers in segment)

Seg.CN (log2() -1 of copy number)

Required as GISTIC2 input?

Also could you please give me an idea how I could install GISTIC2?

Thanks a lot in advance


Sign In or Register to comment.