Closed omarkr8 closed 2 years ago
--help
--min_depth nucleotides below min depth will be masked to "N" [default 20]
Thanks, I did manage to find it in documentation. Just wasnt sure how the min_depth was being used. So for bad runs, reducing the min_depth helps with reducing Ns at the cost of confidence in the consensus.
yes. I also clarified some help messages (available in the next release)
what does the min_depth option do exactly? I imagine it is independent of the min_coverage related to RKI? I also do not see min_depth being referenced when starting the pipeline (unlike other parameters you can adjust).