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  • Variation Callers?

    I am analyzing some whole genome data and at the moment I use GATK for indels and SNPs. What are some other tools or pipelines out there for whole genome analysis?

    For example I read the HugeSeq paper, and I saw pindel, CNVnator, BreakDancer, and BreakSeq. Does anyone have other recommendations or preferences among these ?

    And do you (or how do you ) combine results from two programs, such as UnifiedGenotyper and Pindel?

  • #2
    Hello,

    There is the same topic here: http://seqanswers.com/forums/showthread.php?t=15000, in case it helps.

    There are also SomaticSniper, MuTect & SNVMix (only for SNPs) and VarScan...
    I have not yet any experience in combining results from two programs, so I cannot help, but I am interested in the answer

    Comment


    • #3
      one more for the long list:

      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

      Comment


      • #4
        Real time genomics (rtg) commercial great for trios
        Freebayes
        Samtools

        Are other good tools.

        Comment


        • #5
          Thanks for the replies so far,

          I'm extremely interested in the combinations of tools - like HugeSeq's pindel and unified genotyper combo - that people think form really comprehensive analysis?

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          • #6
            Hi there

            it seems that FreeBayes has not been published yet. Is this so?

            The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.



            Thanks

            Dave

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            • #7
              We are using Platypus (http://www.well.ox.ac.uk/platypus) for our Haloplex panels.

              Comment

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