i have 10 human samples. i have aligned to human grch38 from ensemble using hisat. i want to the sample gender. i have checked reads for X and Y chromosome. For all the samples X reads are greater compared to Y. i refered this link. But our samples have male samples. how is this possible. i dont have the access to GATK DepthOfCoverage. what could be the alternate for this to find coverage. or is there any other way to confirm the gender.
thank you all