So many people have mentioned previously about seeing reads aligned in the Y chromosome when the sequencing data is from a female subject. So there are ways around it, such as masking PAR regions or excluding the Y chromosome from the study completely.
I have the following challenge. What can you do when you use plasma from a pregnant mom, you don't know the gender of the fetus and you are trying to determine:
a) the fraction of the fetal circulating DNA
b) the gender of the fetus
We get reads on the Y chromosome (in non-PAR regions) and we can't predict the gender.
We got the best results by using the old Bowtie version with couple options to align our data, but still can't clearly tell if the fetus is a male or female.