vcfhacks

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.

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

Project Activity

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License

GNU General Public License version 3.0 (GPLv3)

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