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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
MIT License
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Sex QC for one sample #116

Closed solcos closed 10 months ago

solcos commented 11 months ago

Hello! I am new to Somalier and I'm trying to perform a sex determination for one sample in a BAM file.

I am getting the next plot for sex determination. image

I am wondering if this is the expected result, compared to the one you provide in github "https://brentp.github.io/somalier/ex.html" it seems biased in some way. And also if there is a way to have a better result, if that is the case. Should it be a good approach to add 'control' samples in it? Or do you know a better approach to perform the sex determination QC?

Thanks in advance!

brentp commented 11 months ago

Hi, can you share your html file? It looks like you have only 2 het sites on X which would indicate that it is nearly certainly XX.

solcos commented 11 months ago

Hello! In case there is something sensitive, can I share it by email?

brentp commented 11 months ago

yes: bpederse@gmail

brentp commented 11 months ago

@solcos I never got the email.

solcos commented 11 months ago

Sorry for the delay. I just sent an email to "bpederse@gmail.com" with the file. Thanks!

brentp commented 11 months ago

Hi, I had a look at the file, this sample must be XX. There are plenty of hom-ref and hom-alt sites on the X chromosome. You might want to check for large structural variants on X to account for the lower coverage or run a tool like indexcov if this is WGS. If it's exome, then it's not too suprising that the coverage is off. Hope this helps, -Brent

solcos commented 11 months ago

Thanks I will do that and take a look at them. Thanks!