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vcfhacks

simple to use commandline programs for VCF filtering and manipulation

As of 2015-10-13, this project may now be found at https://github.com/gantzgraf/vcfhacks.

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Description

PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/vcfhacks) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/vcfhacks/releases/latest).

(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

Features

  • 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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Additional Project Details

Programming Language

Perl

Registered

2013-11-18

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