Can SplitSamFile split by lane instead of by subject?

stechenstechen University of PennsylvaniaMember

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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