I have used bcftools +guess-ploidy on some of the vcf files but every sample is predicted as females. How to correct this? Or any other easy method available to guess the gender based on exome data. Thanks in advance.
We used plink's --check-sex option based on a reliable set of SNPs on chrX and chrY. Not sure how different that would be from the guess-ploidy extension
Have you confirmed that your samples have significant # of reads aligning to the Y chromosome?
I had seen 10k reads aligned to y for a female exome data. I don't know the cutoff for number of reads to consider to be significant or not.