Best practices for splitting unmapped BAM files

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Lindo Nkambule

• January 05, 2024 17:02
• Edited

Hi GATK Team,

I have ~350 BAM files that are about 150GB each in size. I have been using some of the GATK workflows as a reference but the SamToFastqAndBwaMemAndMba (mapping reads to reference) step is taking a while and I was wondering if there are best practices on how one should be splitting a BAM so they can run the mapping in parallel over multiple chunks?

Thank you,

Lindo

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  Laura Gauthier

  • January 08, 2024 20:56

  Hi Lindo Nkambule,

  Alignment does take a long time. The Terra workspace says to expect 6.5 hours (but only $0.40) for the down sampled data in: https://app.terra.bio/#workspaces/warp-pipelines/Whole-Genome-Analysis-Pipeline/data. That smaller dataset could be a good way to test your pipeline.

  -Laura

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