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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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Why this is a male? #125

Closed solcos closed 9 months ago

solcos commented 9 months ago

Hello!

I run somalier in a sample and this is the somalier.samples.tsv file output.

image

Why this is a male, if it does not have any sites in the Y chromosome? I understand that it has be thanks to the X chromosome depth though. Am I correct?

Thank you very much!

Arnau

brentp commented 9 months ago

Hi, the checks for that are here: https://github.com/brentp/somalier/blob/7740a33a2a0ae35302d223e9dbf14f7e2c353cd5/src/somalierpkg/relate.nim#L517 and here: https://github.com/brentp/somalier/blob/7740a33a2a0ae35302d223e9dbf14f7e2c353cd5/src/somalierpkg/relate.nim#L522

so it's checking what the ratio of het to hom_alt sites on the X chromosome.

It's likely best to do this your self using the HTML output and checking the 2 links that show different sex QC plots.