Using stacks on mixed-ploidy hymenopteran data?

[Claude Patrick Millet]

Hello all,

I am gearing up to analysis RADseq data (paired-end, EcoRI-cut) from a parasitoid wasp species in order to determine genetic structure and perform landscape genomics analyses. I know that among my data are males, females, and samples of unidentified sex. In many hymenopterans including my species, males are haploid and females diploid. I am of course intending to perform post-VC analyses separately for males and females. My plan is however to perform de novo SNP calling using Stacks on all my samples, then use differences in heterozygosity (which should be zero in males, save for errors) to sex my unidentified samples. I was wondering if there were any counter-arguments or red flags around using stacks for variant calling on a mixed-ploidy sample set? I saw this previous discussion but

there isn't a whole lot in that thread. Anybody have experience trying such an analysis?

Thanks!

Patrick