For individuals with no Y chromosome inferred, we will realign X and Y reads just to the X chromosome.
For individuals with a Y chromosome inferred, we will realign X and Y reads to both the X and the Y chromosome, but with shared X-Y regions masked out of the Y chromosome (so reads won't be split between the two chromosomes, and we can improve variant calling.)
I need to look into how the XTR aligns on the X and Y in samples with and without a Y chromosome.
For individuals with no Y chromosome inferred, we will realign X and Y reads just to the X chromosome.
For individuals with a Y chromosome inferred, we will realign X and Y reads to both the X and the Y chromosome, but with shared X-Y regions masked out of the Y chromosome (so reads won't be split between the two chromosomes, and we can improve variant calling.)
I need to look into how the XTR aligns on the X and Y in samples with and without a Y chromosome.