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!

When to use BQSR?

snwilliams88snwilliams88 University of North Carolina at Chapel HillMember
edited May 2015 in Ask the GATK team

Hi,

I am new to NGS/GATK & have a paired-end targeted (targeted to 1 region on 1 autosome) illumina sequencing project on roughly 470 samples. I was wondering whether Indel Realignment & BQSR were appropriate for my setting, or what considerations should be taken into account when judging whether these steps are appropriate?

I'm curious because I noticed this text here:
Small targeted experiments
The same guidelines as for whole exome analysis apply except you do not run BQSR on small datasets.

I was unsure whether my project qualified as a 'small dataset' where BQSR should not be run.

Thanks for any help you may be able to offer!

Answers

Sign In or Register to comment.