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Summary of multi-sample VCF

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  • Summary of multi-sample VCF

    All,

    Does anyone know any tool that can summarize the variants in a multi-sample VCF file? I would require a table format summary of variants that shows:

    a) #novel
    b) #dbSNP
    c) dbSNP_%
    d) #heterozygous
    e) #homozygous

    for each sample as columns:

    Any suggestion would be useful.

    Raj

  • #2
    You probable wont find such package.
    But https://sourceforge.net/projects/vcf-summarize/
    can help you extract any field in a multisample vcf and automize summarization and plot

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