simple to use commandline programs for VCF filtering and manipulation

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(relatively) Simple to use commandline tools for the manipulation and analysis of VCF files, geared towards the identification of pathogenic mutations in Mendelian disease.

vcfhacks Web Site


  • filter SNPs on minor allele frequency and/or SNP build
  • filter on EVS minor allele frequency
  • filter on allele frequency in other VCFs
  • filter on samples
  • find biallelic (compound het or homozygous) variants in one or more samples/families
  • find de novo variants
  • annotate gene information to VEP output
  • write output summary to .xlsx spreadsheet

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