`goleft covstats` with low-coverage cram files output a 0.00 mean coverage

[LouisLeNezet]

Hi,

I've been using goleft covstats for my analysis on low-pass sequenced data and it worked well with bam files. I've recently however moved to cram files and even if the tool worked with the -f option for the fasta, the mean coverage is at 0 for all my samples whereas they should be around 0.5 / 1 X. I've tried restricting the computation to a few chromosomes with the -r arguments but it didn't change.

Do you know what I might have done wrong ? Thanks

[brentp]

hi Louis, the coverage part of covstats won't be reliable for cram. for low coverage, you should be able to run mosdepth on cram in a few seconds. it will use, comparatively, a lot of memory, but still very fast.

[LouisLeNezet]

This is what I did. It's just that the covstats function was really fast and efficient for what I needed. But if it's not possible I will use mosdepth.