Read Groups from SplitSamFile

Hi,

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.

Thanks

Daniel

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,173Administrator, GATK Dev admin
    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.

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,173Administrator, GATK Dev admin
    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.

    Geraldine Van der Auwera, PhD

  • dklevebringdklevebring Posts: 79Member

    One more thing regarding SplitSamFile: The walker does not currently index the bam files it outputs, like the other walkers do. Is that intended?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,173Administrator, GATK Dev admin

    Nope, it seems this is a bug -- thanks for reporting, we'll fix it for the next release.

    Geraldine Van der Auwera, PhD

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