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.
Attention:
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.

CalculateContamination on non-tumour samples

I have seen that calculate contamination is part of a somatic workflow but is there any reason that it cannot be used on germline samples to detect potential contamination (in tumor-only mode?).
Apologies if this has been answered elsewhere. I wasn't able to find anything when I looked.

Answers

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @sararar You may use CalculateContamination in tumor-only mode as you described on a germline sample. However, since it's a cancer tool that needs to work well even in a sample with lots of copy-number variation it is very cautious about ploidy. Germline contamination tools generally assume the sample is diploid, which adds power when it's true. I wouldn't worry about this if it's much more convenient to use CalculateContamination but I also don't want to give the impression that we have replaced tools like VerifyBamID, at least not until we set up an evaluation that shows this.

  • sarararsararar Member
    Thank you. We have been using verifybamid, however it is showing high levels of contamination in most of the samples we run on an Illumina NextSeq. As it is not likely that all of the samples on several runs are contaminated I am looking for another tool.
Sign In or Register to comment.