The current GATK version is 3.2-2

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Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

Posts: 68Member

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

Tagged:

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