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  • mrxcm3
    Junior Member
    • Oct 2010
    • 9
    #1

    SNP calling software in pooled samples

    I have some very deep seq data for a small genomic region (50kb) - generated in pooled samples using SOLiD - and I am looking to discover rare variants.

    Can anyone recommend any good SNP callers for pooled data? So far I have tried GATK (which is not suitable), VarScan, Syzygy and standard pileup (samtools). Anyone able to suggest other I should check out? Thanks
    Tags: None
  • lh3
    Senior Member
    • Feb 2008
    • 686
    #2
    http://genome.cshlp.org/content/early/2010/11/01/gr.109157.110.abstract

    Comment

    • krobison
      Senior Member
      • Nov 2007
      • 734
      #3
      The list in the software wiki is always growing (category: SNP discovery. It might be worth having a second category for ones which work on pools -- I'm sure there are some you haven't listed (though I have not tried any of them).

      It looks like SNPSeeker and CRISP definitely fall in that categoryl; I think QCALL is not in this space but I could easily be wrong.

      Comment

      • Jose Blanca
        Member
        • Aug 2009
        • 70
        #4
        The exactly same topic has been discussed in the samtools list a couple of days ago.

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