Harriet Dashnow

Good idea adding that filter. It made the estimates *slightly* smaller. e.g. 33.04 instead of 33.4. Still nowhere near Picard.

P.S. I think I've figured out how to calculate median coverage from the mosdepth output. It's not as fast as covstats, but still faster than most other tools out there.

Much appreciated, thank you!

I've also been thinking about this for the purposes of deciding on an output VCF format for STRling (https://github.com/quinlan-lab/STRling) Adding to this, it would need a repeat unit(s) and ideally...

Here's a made up toy example to replicate the error: ``` import sys import pyranges as pr # convert all warnings to errors if not sys.warnoptions: import warnings warnings.simplefilter("error") a...

Yep. So if that's invalid input then an error stating that would be more useful. At the moment it gives a warning that isn't clear.

I think a validity check that reports offending rows would be very useful. You could also force an error (rather than warning) in situations where divide by zero is possible,...

For 3. consider two SVs/STRs in the same gene as well.

Hi @baoyl818, Thanks for reporting this. Let me see if I can replicate the error, and I'll get back to you. Warm regards, Harriet

Would you mind running the install test to see if that works? https://github.com/Oshlack/STRetch/wiki/Installing-STRetch