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epi2me-labs / wf-human-variation

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CRAM or BAM output #158

Closed asalhab closed 3 months ago

asalhab commented 3 months ago

Ask away!

Hi, As I understood from the documentation, CRAM will be generated by default unless --cnv was used then a BAM will be generated. I ran v1.9.1 on different samples with the exact command (including --cnv) and the coverage of the samples was above 20. Nevertheless, sometime I get CRAM and sometimes a BAM. Do you have any idea what could be the reason for that? Can I force the pipeline to always produce a BAM as there are QC tools don't accept CRAM yet? Thank you !

RenzoTale88 commented 3 months ago

Hi @asalhab, we normally create a CRAM file as an output to avoid inflating the work directory. The only exception is, as you noticed, when a user selected --cnv, as QDNAseq requires the input to be in BAM format.