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  • mmmm
    Senior Member
    • Jul 2013
    • 131
    #1

    Perl script

    could I get the perl script that can be used to determine the effect of SNPs when comparing large number of samples-
    I have (output.vcf) and would like to get (snp_report.txt) so it can easily show difference between strains
    Tags: None
  • dGho
    Member
    • Jan 2013
    • 43
    #2
    You question is a bit vague. What specifically are you looking to include in the snp report? the number or snps per sample?

    Comment

    • mmmm
      Senior Member
      • Jul 2013
      • 131
      #3
      the script with the output vcf file takes the information from the reference fasta and annontation gff files to determine if the snps occur within a gene and shows the snp effect (silent, indel, ...)

      the command should be like this:

      script ref.fn ref.gff vcf file > snp-report output file

      the output file contains the following 6 columns:
      chrom pos ref nucleotide snp(in vcf) gene name snp status

      Comment

      • dpryan
        Devon Ryan
        • Jul 2011
        • 3478
        #4
        Presumably that's either variant effect predictor or snpeff.

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