There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting, and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project.Source…
G T A T C G C T A
GATK-Queue
Cloud

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

G T A T C G C T A
VCFtools
Desktop

VCFtools

A program package designed for working with VCF files, such as those generated…

A program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex…

G T A T C G C T A
Joinx
Desktop

Joinx

A lightweight tool for performing operations (e.g., intersection, difference,…

A lightweight tool for performing operations (e.g., intersection, difference, …) on genomic data contained in .vcf and .bed files. Joinx also provides some limited analysis functions (concordance…

G T A T C G C T A
MuCor
Desktop

MuCor

A flexible tool for variant aggregation and summarization. A key goal is…

A flexible tool for variant aggregation and summarization. A key goal is generality, that it may replace the ad hoc scripting often performed in the course of routine bioinformatic analyses of…

G T A T C G C T A
VTC
Desktop

VTC Variant Tool Chest

Provides a variety of tools for manipulating, comparing, and analyzing VCF…

Provides a variety of tools for manipulating, comparing, and analyzing VCF files beyond the functionality of existing tools. In addition, VTC was written to be easily extended with new tools. Variant…

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