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.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

how I interpret the genotype result?

love_boneslove_bones chinaMember
edited August 2016 in Ask the GATK team

Dear all,
Follow the GATK best practice, I got one sample with the genotype 0/0:47,0:49:99:0|1:131931451_TA_T:0,141,1807 in the vcf file. According to the format column GT:AD:DP:GQ:PGT:PID:PL, this item can be interpreted as:

GT: 0/0
AD: 47,0
DP: 49
GQ: 99
PGT:0|1
PID: 131931451_TA_T
PL:0,141,1807

I know the PGT and PID are new tags for physical phasing (http://gatkforums.broadinstitute.org/wdl/discussion/4682/pgt-and-pid-in-vcf). But I do not understand is why the GT(0/0) is not the same as the PGT(0|1).

The GATK version is 3.6-0-g89b7209.

Thanks.

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @love_bones
    Hi,

    Can you please post IGV screenshots of the original BAM file and bamout file in the region? Please include the sites that are phased.

    Also, please post the exact VCF records of the two phased sites in question. The sites that are phased will have the same PID.

    -Sheila

Sign In or Register to comment.