Is there any package available for SNP/Indel annotation?

[Ling]

I got a lot of SNPs and Indels from the Illumina sequencing data of an Arabidopsis plant mutant. To identify the candidate mutations I have to first screen these polymorphisms to see whether and which genes these polymorphisms are located at and what changes these mutations caused at amino acid level.


It will be really tedious if it has to be done manually.

Does anyone know if there is any computational tool available for SNP/Indel annotation?


Thank you

Ling

[Natalya]

The best way, programing.
An simple PERL program can help you done the job.

[krobison]

You might look through all the SNP tools in the software wiki. Certainly they (and tools such as BEDTools) will let you xref your variants against known variants.

[Ling]

Hi Krobison,

Thank you very much for your suggestion! I will explore it.


Ling