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Read Groups from SplitSamFile


If I have a bam file with three different read groups, and use SplitSamFile to split it like so:

java -Xmx2g -jar $GATKJAR -T SplitSamFile -I $INBAM -R $GENOME --outputRoot $PROJD/$IND/

Each of the output bam files have all three read groups. Is that the intended behavior? I would like each file to have only it's own read group info in the heads. Sorry for the bash arguments in the code above, is makes in readable at least.



Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Hi Daniel,

    From the code it looks like SplitSamFile is indeed not tasked with updating the headers. I'll check if that's really what we want and if not, we'll patch this up for the next version.


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