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genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.
MIT License
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Account for CRAM conversion. #41

Closed jasonwalker80 closed 7 years ago

jasonwalker80 commented 7 years ago

We either need to:

  1. Natively support CRAM throughout the workflow
  2. Convert back to BAM first thing
  3. Convert back to BAM only for steps that require BAM instead of CRAM
jasonwalker80 commented 7 years ago

Samtools/VarScan has no problem with CRAM inputs instead of BAM.

jasonwalker80 commented 7 years ago

Strelka works just fine with CRAM inputs instead of BAM.

jasonwalker80 commented 7 years ago

Mutect also works with CRAM, no surprise there.

jasonwalker80 commented 7 years ago

Pindel works, but instead of using the samtools default index of .cram.crai Pindel only looks for the CRAM index as ^.crai without the .cram extension in the path.