Sex chromosome filtering/Sex linked SNPs filtering

Question

[safiq713]

Dear All,

I am new in NGS analysis. I have 90 samples ddRAD data. I am using reference based analysis.

In my samples some samples are male some are female. I want to structure analysis. before doing structure analysis I want to filter or remove heterogametic SNPS. (Male has ZZ and female ZW chromosomes). How can I remove sex linked SNPs from my data to do structure analysis.

Could you please suggest me which tool I should use? Do you know any example.

Thanks a lot for your kind help.