Sex determination Option

[maxulysse]

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]

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]

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