Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

BaseRecalibrator documentation missing -BQSR argument

igorigor Posts: 31Member
edited July 2013 in Ask the 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

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