Brent Pedersen

Hi, I have known there are some issues with the somalier ancestry setup. You can trust the peddy ones (as you note) much more. For somalier, I would use `--n-pcs...

Is your data from sequencing? Exome? WGS? Or from a chip?

Hi, I see what you mean. Can you run `somalier relate` with `--min-depth 5` and let me know if the result matches more what you expect? With a cutoff of...

Indeed, that rules out my guess. Is there any chance that you can share the extracted .somalier file? I think it is odd that there are so many `n_hom_alt`, +...

Thanks for the clear report. It seems likely that there's something with somalier. I expect it's easily fixed, but I'll have to find the problem. I'll check for a few...

> Can you elaborate on this, I'm not quite getting the point: > > > there are other problems with somalier not having enough info about hom-ref Actually, that's just...

I'm really confused about what's going on. This is showing a much lower depth from DeepVariant calls. The ratio of homalts is dramatically reduced from DV indicating there could be...

So, mosdepth shows about the expected coverage ratios for a male, though the X is a bit high. DeepVariant+somalier does not so it's not a problem to specific to how...

I think there is some bias with higher coverage near start of the chromosomes. I will look into this next week. Thanks very much for following up. Should have a...

you could also try: https://github.com/brentp/somalier/files/4566475/sites.hg38.rna.vcf.gz but I will have a look at this problem.