Remove SNP in segment duplication and repeat region

[cindylanzao]

Hi，All

I am trying to detect somatic mutations in healthy people, I have searched some reference, however, both of the two detection method contains remove those variants in segment duplication and repeat region. Can anyone explain why should remove those SNP located in these two regions? Thanks!

[wdecoster]

In short, because those variants have (due to technical difficulties) a high chance of being false-positive.

[cindylanzao]

In short, because those variants have (due to technical difficulties) a high chance of being false-positive.

Thanks, could you explain a little bit of why variants in these region could be false-positive?

[Brian Bushnell]

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.

[cindylanzao]

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