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.
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!
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!
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!
CombineGVCFs does not work on haploid genotypes
blueskypy
Member ✭✭
It converts a haploid genotype 0 or 1 to a dot; for example:GT:DP:GQ:MIN_DP:PL 0:53:99:18:0,666 to .:53:99:18:0,666
Answers
IIRC, this is intended behavior, and happens with any ploidy. GVCFs are not intended to be used as final calls, and GGVCFs doesn't use the genotype field
hi, @pdexheimer
Thanks for the quick response! I'm going to feed the combined gvcf file to GenotypeGVCFs. If GenotypeGVCFs does not use the GT field, what field is used?
PL. It's all likelihood-based, which is where the benefit of joint calling over naive conglomeration comes in
I see, thanks a bunch! @pdexheimer