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  • mmarti12
    Junior Member
    • Aug 2015
    • 2
    #1

    Alignment tool that lists SNPs?

    Hello,
    I'm going to do GWAS among a subset of bacterial genomes that have a specific phenotype and I was wondering whether there's a tool that gives you the list of snps among them. I wouldn't like to use a reference to find the variations because in this case I'll miss the comparison of the genes that are not present in the putative reference. So I excluded comparative software like breseq.
    Any suggestions?
    Thanks a lot
    Tags: None
    • JohnN
      Member
      • Jan 2011
      • 31
      #2
      ParSNP from the Harvest suite?

      Harvest — harvest 1.0 documentation
      https://harvest.readthedocs.org/en/latest/

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