Hi,
I have some mouse samples. I would like to determine sex to test for sample switch or corruption from sequencing data. I have vanila freebayes called vcf files. I figured out that there is plugin to determine sex from vcf files

    bcftools +vcf2sex

However it seems to require ploidy information for given genome(see for example this problem https://github.com/samtools/bcftools/issues/175). This information should be in the format 

> space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY

I am using GRCm38.82 (http://ftp.ensembl.org/pub/release-82/gtf/mus_musculus/README) for read mapping and I cannot find that ploidy information for given genome release.

I would like to ask:

 1. Which is most reliable way to determine sex of the sample either from bam or vcf file?
 2. What does exactly ploidy information mean? Are those coordinates of pseudoautosomal regions? And why this information is required for vcf2sex to work properly?
 3. Where can I find that ploidy information for given genome release?
I figured out that for the assemblies there are informations about pseudoautosomal regions available through Genome reference consortium. In case of my genome I had to read this http://ftp.ensembl.org/pub/release-82/fasta/mus_musculus/dna/README to understand that DNA sequence is GCA_000001635.6 which is GRCm38.p4 and then from http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/ I can figure out which are the coordinates of pseudoautosomal regions. From that I can assemble ploidy file that might be

    X       1       169969759       M       1
    X       170931300       171031299       M       1
    Y       1       91744698        M       1
    Y       1       91744698        F       0

However I figgured out the tool works better when using ploidy file of the form

    X       1       169969759       M       1
    Y       1       91744698        M       1
    Y       1       91744698        F       0

When facing this you can also try using this repository https://github.com/pd3/bcftools and plugin called +guess-ploidy
