Nick Harding

Hi @yuan102379 , please see the answer here: https://github.com/hardingnj/xpclr/issues/57#issuecomment-647453586 and https://github.com/hardingnj/xpclr/issues/59#issuecomment-664436938

Hi @hungweichen0327 1. Yes- that is correct. If you use a VCF you can skip the map requirement using `-rrate` 2. The calculations in xpclr are reasonably robust to recombination...

It looks like because you have no eligible SNPs in the windows before 35_000. The final window is normalised to 0.0, as that is the only window with an XP-CLR...

Sorry for the slow response: What system are you running on? Did you install via `conda` or `python setup.py install`?

I think this is an issue with the way filepaths are set up in your environment. Are you sure you are using the correct version of python on your system...

Apologies. I think I would interpret results of highly inbred populations with extreme caution. XP-CLR identifies regions of the genome that have drifted more than you would expect under neutral...

Hi Janet. Interesting problem. As XPCLR only requires population allele counts, the triploid should work fine. VCFs are read in using scikit- allel which supports multiple ploidy. I'm also not...

Thanks Janet- that's interesting I would have assumed it would be read at ploidy=3. As a hack, as it only counts the alternative aleles, as long as the ratios are...

Thanks, this certainly looks like a bug. Though not one I can immediately identify. Let me look into it!

Thanks. Looks like the same bug: https://github.com/hardingnj/xpclr/blob/a555c442b6ce9deff5ecff6e3080a5bde0acb557/bin/xpclr#L57 Seems that LD should be interpreted as a float, but something is not correct.