How to handle allosomes and chrM in GATK?

Question

[Arup Ghosh]

I'm using whole-genome sequencing (human) data for variant calling using GATK HaplotypeCaller. By default, the HaplotypeCaller returns diploid calls on all the chromosomes, but for male haploid call should be made for chrY, non-pseudoautosomal chrX and chrM/chrMT for both male and female. So, when dealing with these calls should I use these regions as intervals in HaplotypeCaller and run using ploidy=1?

The 1000 Genome project (Phase 3) method section(supplementary info page 78) they have mentioned about following a different protocol for chrY but the details are not very clear to me.

[finswimmer]

Doesn't answer your question for using HaplotypeCaller., but as an alternative have a look at bcftools. There you can define the ploidy based on region and sample sex. See the description of --ploidy-file and --samples-file here.