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  • foxyg
    Member
    • May 2010
    • 54
    #1

    What are the SNP calling programs?

    Hi guys,

    What are the popular SNP calling programs out there. I tried samtools, and GATK, are there any other good ones out there?

    Thanks
    Tags: None
  • krobison
    Senior Member
    • Nov 2007
    • 734
    #2
    I've been using SNVMix, but haven't tried to benchmark it.

    Other tools can be found here.

    Comment

    • Jose Blanca
      Member
      • Aug 2009
      • 70
      #3
      We have an SNP caller deveped to call and filter highly reliable SNPs to be used in genotyping experiments. You can take a look at ngs_backbone.
      We have experimentaly validated the result in a tomato experiment and we have obtained very good results.

      Comment

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