genotyping sex chromosomes
Hi GATK team,
I have exome samples, some males and some females.
I mapped the female to a reference genome without the Y chromosome, and continued with each sample the Best Practice steps.
The reason for that mapping is that we don't want to lose some of the females reads to the homologous regions of chro Y.
Will I be able to run GenotypeGVCFs on those samples?
Is this a good way to do the genotyping on the sex chromosomes?
thank in advanced,