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

Comments (0)

A new tool has been released!

Check out the documentation at SplitSamFile.

No posts found with the requested search criteria.
Comments (2)

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

Comments (1)


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

Comments (3)


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.