vcfhacks

simple to use commandline programs for VCF filtering and manipulation

Status: Alpha

Brought to you by: gantzgraf

As of 2015-10-13, this project can be found here.

Downloads: 0 This Week

Last Update: 2015-05-08

Get an email when there's a new version of vcfhacks

Linux

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

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow vcfhacks

vcfhacks Web Site

Other Useful Business Software

Gen AI apps are built with MongoDB Atlas Icon

Gen AI apps are built with MongoDB Atlas

Build gen AI apps with an all-in-one modern database: MongoDB Atlas

MongoDB Atlas provides built-in vector search and a flexible document model so developers can build, scale, and run gen AI apps without stitching together multiple databases. From LLM integration to semantic search, Atlas simplifies your AI architecture—and it’s free to get started.

Start Free

Rate This Project

Login To Rate This Project

User Reviews

Be the first to post a review of vcfhacks!

Additional Project Details

Operating Systems

Programming Language

Registered

2013-11-18

Report inappropriate content

Recommended Projects

PhyloTrack
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples,...
HRVAS: HRV Analysis Software
This project will be moving to GitHub. If you want to contribute or get the latest source go to: https://github.com/jramshur/HRVAS HRVAS is a heart rate variability (HRV) analysis tool developed using MATLAB. HRVAS can detrend and filter IBI and can perform time domain, frequency domain,...
Mutation Mapper
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.
DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each...
MToolBox
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an...