auto gender detection assignment for reference creation problem

[duartemolha]

Hi,

I'm encountering an issue while creating a reference from a sequencing panel that includes targets on both chromosome X and Y.

During the reference creation step, the infer_sex method determines the sample's ploidy differently based on targets and antitargets. Specifically, it identifies an XY (male) ploidy for the targets but an XX (female) ploidy for the antitargets. This results in the following log message:

**Sample NNN chromosomal X/Y ploidy looks like male in targets but female in antitargets; preferring antitargets.**
According to the do_reference function, the final sex determination follows the antitargets. However, in my panel, this decision seems to be incorrect, as the samples are indeed male (as confirmed by the targets).

Can someone explain why the method defaults to antitargets instead of targets for sex determination? Since targets are specifically baited and captured, while reads in the antitargets arise from imperfect capture, it seems like target data would be more reliable. For instance, female samples should have no captured reads on chrY targets, and males should always have some, unless there is a CNV deletion.

I understand that I can manually specify the sample sex, but I'd like to understand the rationale behind this behavior, and why my male samples are being assessed as XX ploidy based on antitargets.