WES chromosome Y off-target reads coverage compare to autosome

Question

[hujingchu]

Hi all, I have couple of WES samples using different capture kits, and would like to predict their gender by evaluating the off-target reads from chromosome Y and autosome(like chr20), some thing strange is the off-target reads per 1M of chrY is always only 10% of autosome(chr20 here), which is far away from my expectation (50%) in Male. Is there any explanation why this happend ?

Answer 1

[markus.riester]

Should be much lower because of the very low mappability of chrY. If you have WES, then why using off-target reads? For most kits, you will have plenty of perfectly mapping exons that will show 0 reads in females (or very few in case of minor cross-sample contamination).