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  • ramouz87
    Member
    • Oct 2009
    • 35
    #1

    Single nucleotide polymorphism (SNP) discovery in polyploid

    Hi,
    I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
    If not, anyone know how to compute SNP confidence score from concensus call in this case ?
    Thanks in adavnce for your suggestions
    Best,
    Ramzi
    Research Scientist - Bioinformatics
    Sidra Medical and Research Center
    Tags: None
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283
    #2
    Originally posted by ramouz87 View Post
    Hi,
    I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
    If not, anyone know how to compute SNP confidence score from concensus call in this case ?
    Thanks in adavnce for your suggestions
    Best,
    Ramzi
    Not too sure, but what about the "-N" option in "samtools pileup"? I say I am not too sure since I am not sure how SNPs with one out of N copies will be reported (N>2).

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