PAR masked or unmasked for aligning PacBio?

[QichenFU]

If I wish to align PacBio reads to CHM13, should I use PAR masked CHM13 or unmasked one?

[arangrhie]

Hi @QichenFU,

If you'd like to integrate results from short-reads, I would suggest to use the PAR masked version for the XY individuals, and use the Y masked version for XX individuals.

Best,
Arang