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.

BQSR with intervals & cut-off base coverage or interval average coverage

manolismanolis Member ✭✭
edited May 2018 in Ask the GATK team

GATK4.0.4.0, scattering

Hi,

if I'm correct:

when I process in the BQSR an interval with very low coverage (0x - 3x base coverage), then I have the error "RecalibrationReport - Missing read group(s) ..." if I go forward to the HaplotypeCaller I have a new error "USER ERROR ... Interval/contig... loci" ...

When the coverage is high everything is ok.

If the above "relation" between errors and steps is correct... what happen when I have two target regions inside an interval, one with a high coverage and the other one with a very low coverage? I lose both regions data or only of the not well covered?

What is the cut-off of reads/coverage/base coverage of BQSR, or average coverage of the inteval?

Many thanks

Answers

Sign In or Register to comment.