Tagged with #splitsamfile
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Created 2012-07-23 23:56:57 | Updated 2012-07-23 23:56:57 | Tags: gatkdocs splitsamfile
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A new tool has been released!

Check out the documentation at SplitSamFile.

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Created 2014-02-26 14:52:51 | Updated | Tags: 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

Created 2013-10-16 16:55:48 | Updated | Tags: splitsamfile
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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

Created 2013-09-05 10:17:13 | Updated | Tags: splitsamfile gatk2 bam
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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.