testrun for region chr1:1000-2000 takes ages

[robertzeibich]

I just wanted to try mosdepth on some of my smaller deletions:

mosdepth --by <(echo -e "chr1\11869\t12227") mosdepth-test-out --d4 -t 4 -f $FASTA $BAMFILE

The command takes for ages. Do you know why?

[robertzeibich]

I got the following output for the following region:

mosdepth-test-out.regions.bed.gz
chr1 11869 12227 78.96

Is 78.96 good?

Goal: I am just trying to generate some extra information to interpret/filter my smaller deletions, insertions and duplications. If you have a better idea, please let me know.

[brentp]

--by just tells mosdepth that you want extra information for those regions or that region. But it must still read the entire chromosome. It's built to be fast on whole-file operations, not on select regions.

I think you can use duphold along with visual plots to evaluate smaller deletions. Duphold will be less reliable the smaller the event, but there should still be signal.