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Old 05-15-2012, 09:29 AM   #1
Location: New York, NY

Join Date: Oct 2011
Posts: 41
Default Is GATK Indel Realigner read group aware?


I want to realign a multi-sample BAM using the Indel Realigner for eventual SNP-calling. I am following the GATK's "Best Practice Variant Detection with the GATK version 3" which recommends running indel realignment on all samples jointly as best practice. It does not explicitly state whether the RealignerTargetCreator and IndelRealigner is readgroup aware.

Does anyone know if the indel aligner is readgroup aware?


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