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Old 03-31-2010, 12:54 PM   #1
dvh
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Default exome indel annotation

Hi,

Can anybody point me to good tools for annotating small (<15bp) indels from human exome resequencing.

Effect on protein coding sequence (frameshift/stop, in frame), known in dbSNP, etc.

thanks

dvh
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Old 04-01-2010, 11:20 AM   #2
bioinfosm
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I know of a software from seattle group, linked to SeattleSeq annotation. Not sure how useful it is, but worth a check.

sm
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Old 04-01-2010, 12:05 PM   #3
dvh
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thanks sm, in fact we are already using seattle seq annotation for SNPs, and it is great.
Doesnt do small indels though - at least not on the public site...?
dvh
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Old 04-02-2010, 06:32 AM   #4
Dongliang Ge
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You may want to check out SVA, a tool that we have been developing:

http://www.svaproject.org

Here is an introduction to an exome resequencing project:

http://www.svaproject.org/capture.php

Annotation categories:

http://people.genome.duke.edu/~dg48/...rianttypes.php



Cheers,

Dongliang


Quote:
Originally Posted by dvh View Post
thanks sm, in fact we are already using seattle seq annotation for SNPs, and it is great.
Doesnt do small indels though - at least not on the public site...?
dvh
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Old 10-07-2010, 01:14 PM   #5
bioinfosm
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Quote:
Originally Posted by dvh View Post
thanks sm, in fact we are already using seattle seq annotation for SNPs, and it is great.
Doesnt do small indels though - at least not on the public site...?
dvh
noticed seattleSeq does take as input GATK bed files for indel annotation now!
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