Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

My ReadPosRankSumTest (ReadPosRankSum) distribution looks funny

JulsJuls Member ✭✭

Hi,

I was looking at the hard filtering cutoffs and hence looking at the distributions of MQ, QD, MRankSum and so on. All look fine - similar to yours (https://software.broadinstitute.org/gatk/documentation/article.php?id=6925) but one. I was wondering wether my ReadPosRankSumTest (ReadPosRankSum) distribution looks indeed funny or if there is a specific reason for that.
Thanks!

Tagged:

Best Answer

Answers

  • JulsJuls Member ✭✭
    edited April 2018

    Hi Sheila,
    Thank you for you answer. It's standard Illumina data. HiSeq 2000. What kind of "quirk" could it be? Any suggestions as to the cause? So you think I could just ignore it? I figured I use a more stringent cutoff e.g, -2.5.

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Juls
    Hi,

    I don't want to say you can ignore it for sure.

    Have you done any QC on your data? For example, have you checked the coverage, contamination, chimerism, and sequencing artifact metrics?

    Is this human data? Have you done some concordance tests against truth sets?

    Thanks,
    Sheila

Sign In or Register to comment.