Post by pae on May 7, 2020 1:42:06 GMT
Hi, when I ran my data (Drosophila data, 900 samples with ~200K markers) using --nofilters, the vast majority of markers were filtered out (only ~15K kept, resulting in gigantic IBD segments). However, when I used --maf .001 --missing 0.999 it kept all the markers and found reasonable segments. Using --maf 0 and --missing 1 resulted in all markers being excluded. It seems like something funny might be going on with these filter flags, but it is working for me now with these tweaks!