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  • gfmgfm
    Member
    • Jun 2010
    • 64
    #1

    extracting info from VCF files

    Hi all,

    I have a vcf file with multiple samples.
    Are there any existing tools to extract basic info, such as:
    Number of SNPs called in each sample?

    I guess it is easy to use command lines, but thought there might be tools that does this and more than that...
    Tags: None
    • gaffa
      Member
      • Oct 2010
      • 82
      #2
      You probably want to look into VCFtools (http://vcftools.sourceforge.net/). It's mostly for management/handling of VCF files, but it can also compute some basic stats on files, and can piped together with shell commands for more power.

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