The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.

BaseRecalibrator documentation missing -BQSR argument

igorigor New YorkPosts: 42Member
edited July 2013 in Ask the GATK team

In GATK 2.6, there have been some changes to BaseRecalibrator. Based on the AnalyzeCovariates page, it must now be run twice. To generate the first pass recalibration table file, it's the same command as before. To generate the second pass recalibration table file, you need to add the -BQSR argument. However, on the BaseRecalibrator page, there is no -BQSR documentation.

Post edited by igor on

Best Answer

Answers

Sign In or Register to comment.