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Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF
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Implement Sex Typing #4

Open brcopeland opened 2 years ago

brcopeland commented 2 years ago

Regardless of whether a PED is provided we should at a minimum be able to infer a sample is from a male, a female, or ambiguous (XO, XXY, XXX). In the latter case we would ideally be able to confidently state what kind of aneuploidy is present, but at least identifying a likely problem would be helpful.

brcopeland commented 2 years ago

I implemented as https://github.com/brentp/peddy does. This is a very simple check that calculates the het:hom ratio for calls on the X chromosome as reported by somalier and if less than 0.6 predicts male and if greater predicts female. Additionally it will send an email if there is a mismatch.

A more sophisticated classifier to infer aneuploidies will require some more thought.

shishenyxx commented 2 years ago

I don't think we need it to be so complicated ... and the more you put there the harder to maintain the codes ...

brcopeland commented 2 years ago

I agree, but it is currently not complicated - it's just that very simple test. I thought you specifically had wanted to detect sex chromosome abnormalities with this.

shishenyxx commented 2 years ago

Yeah, just sex ratio is enough, I thought you want to add a more sophisticated one ...

brcopeland commented 2 years ago

It was just an idea. I have sufficiently many other things going on that it is not a priority, but I thought this would be at least a place to document the discussion.

shishenyxx commented 2 years ago

Totally agree ... that's also why I left some comments last night ...