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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Sex determination Option #98

Open maxulysse opened 4 years ago

maxulysse commented 4 years ago

Issue by @apeltzer, moved from SciLifeLab#688

Is your feature request related to a problem? Please describe.

If you don#t know the sex of an individual, one could run simple scripts to perform sex determination. This is commonly done in population genetics and there are quite a bunch of scripts to perform that automatically, more or less checking chrX/chrY ratios with thresholds.

Describe the solution you'd like

Having an optional step may be to run sex determination, as we do have cases where we don't have the information....

egenomics commented 2 years ago

It is also very useful as a control when running multiple clinical samples. We can cross the expected sex for the sample with the sex determination done to detect possible errors in sample handling / processing.

SusiJo commented 1 year ago

@apeltzer suggested to look at peddy or Sex.DetERRmine which are both already available in MultiQC.