Tagged with #splitsamfile
1 documentation article | 0 announcements | 3 forum discussions


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A new tool has been released!

Check out the documentation at SplitSamFile.

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If I don't provide an output root for SplitSamFile the resulting files include the string 'null'. I believe it shouldn't, right?

Thanks, Carlos

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Greetings!

I have whole genome sequencing data from one individual from 8 lanes of Illumina HiSeq. I was wondering if the SplitSamFile tool can be used to divide the reads by lane number instead by by subject (since I only have one subject). Also, where should I use this tool? Presumably before the RealignerTargetCreator step?

Thank you! Stephanie

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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