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  • Ling
    Junior Member
    • Jan 2010
    • 8
    #1

    Is there any package available for SNP/Indel annotation?

    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
    Tags: None
    • Natalya
      Junior Member
      • Jan 2010
      • 5
      #2
      The best way, programing.
      An simple PERL program can help you done the job.

        Comment

        • krobison
          Senior Member
          • Nov 2007
          • 734
          #3
          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.

            Comment

            • Ling
              Junior Member
              • Jan 2010
              • 8
              #4
              Hi Krobison,

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


              Ling

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