SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Remove SNP in segment duplication and repeat region (http://seqanswers.com/forums/showthread.php?t=75653)

cindylanzao 04-24-2017 05:21 PM

Remove SNP in segment duplication and repeat region
 
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 04-24-2017 10:50 PM

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

cindylanzao 04-24-2017 11:28 PM

Quote:

Originally Posted by wdecoster (Post 206674)
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 04-25-2017 12:12 PM

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 04-27-2017 05:47 PM

Quote:

Originally Posted by Brian Bushnell (Post 206712)
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


All times are GMT -8. The time now is 09:32 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.