should I use HS assembly with ChrY masked or not?
Hi folks,
We have some genes on target panel are on sex chr that we need to generate coverage and call the variants. For example, gene CRLF2 has one allele on chrX and another one on chrY. But the assembly that we are using is 1000 genome hg19 assembly which has chrY masked. So we don't have the coverage of CRLF2 on chrY.
We are wondering if anyone can give us some suggestion, like pros/ cons using hg19 assembly with chrY NOT masked.
Many thanks,
Kajia
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As far as I know, masked is only heterochromatic portion of the Y chromosome. If you look at Y chromosome in your data, how many unmasked [ACTGactg] basepairs do you have?
Well, for the gene CRLF2, its all masked on Y. Not sure if we should use assembly with unmasked chrY for variant call. Any idea?