exome indel annotation

[dvh]

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

[bioinfosm]

I know of a software from seattle group, linked to SeattleSeq annotation. Not sure how useful it is, but worth a check.

sm

[dvh]

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

[Dongliang Ge]

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/sva/varianttypes.php

Cheers,

Dongliang

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

[bioinfosm]

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!