mosdepth exclude soft clipped bases to calculate coverage?

Question

[kani]

Does the mosdepth exclude the soft clipped bases present in the aligned reads to calculate the coverage?

Default it exclude the mark duplicate and secondary alignment reads (-F 1796) and avoid double counting overlapping read pairs.

mosdepth --no-per-base --by 1000 --mapq 20 --threads 4 ${biosample_id} ${bam}

Answer 1

[Pierre Lindenbaum]

Does the mosdepth exclude the soft clipped bases

yes it uses the SAM start position (!= unclipped start) sequtils.to_seq(gen_start_ends(rec.cigar, rec.start.int))

https://github.com/brentp/mosdepth/blob/master/mosdepth.nim#L299

[kani]

Thank you so much