Using CRAM instead of BAM when genotyping samples for SVs?

brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Apache License 2.0

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Using CRAM instead of BAM when genotyping samples for SVs? #153

Closed Saeideh-Ashouri closed 3 years ago

Saeideh-Ashouri commented 3 years ago

Hello.

I have done SV calling using smoove but I do not have enough disk space for storing BAM files for a large number of samples I am working with (12,500 samples). Is it possible to use CRAM files instead when genotyping them for SVs?

Thank you in advance, Best, Saeideh

brentp commented 3 years ago

Hi Saeideh, crams will work fine with smoove.