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Old 04-27-2017, 05:47 PM   #5
cindylanzao
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Location: chicago

Join Date: Nov 2012
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Quote:
Originally Posted by Brian Bushnell View Post
In a duplicated/repeat region, there is no way to know whether the read is mapped to the correct location; and thus, it's impossible to determine whether the variant call is in the correct place. Also, repeats are hard to assemble so the reference is less likely to be correct there. Typically you can just discard ambiguously-mapped reads rather than discarding variants, though.

There's a large block of Chr Y that is similar to Chr X; as an exception, variants in this region are often called on the X chromosome, since if they were discarded, much of the X/Y chromosome would be unusuable for variant detection.
Thanks Very Much
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