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VCF/BCF file manipulation software tools

The variant call format (VCF) has become the standard format for storing variants identified in next-generation sequencing (NGS) and other studies. VCF files are flexible with eight fixed fields including chromosome (CHROM), position (POS), known…
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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of…

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GATK-Queue
Desktop

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…

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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed…

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles…

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Onto-Translate
Web

Onto-Translate

Helps the user with the problem of mapping various types of IDs to each other.…

Helps the user with the problem of mapping various types of IDs to each other. Onto-Translate provides the users with a non-redundant and complete mapping from any type of identification system to…

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SnpEff
Desktop
Web

SnpEff

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs).…

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom…

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vcfr
Desktop

vcfr

Helps users to manipulate and visualize VCF data. vcfr provides ready access to…

Helps users to manipulate and visualize VCF data. vcfr provides ready access to the multitude of statistical and graphical tools provided by the R environment. It contains functions to parse VCF data…

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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…

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SeqArray
Desktop

SeqArray

Stores variant calls in an array-oriented manner which provides the same…

Stores variant calls in an array-oriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access. SeqArray uses high-performance parallel…

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VCF-kit
Desktop

VCF-kit

Analyzes or annotates VCF files and organizes tools that perform diverse…

Analyzes or annotates VCF files and organizes tools that perform diverse analyses using VCF files. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for…

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VCF2RDF
Web
Desktop

VCF2RDF

Identifies a web enabled isomorphic map between Variant Call Format (VCF) and…

Identifies a web enabled isomorphic map between Variant Call Format (VCF) and Resource Description Framework (RDF). VCF2RDF is a VCF parser that acts as an isomorphic mapping function to (evolvable)…

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vt normalize
Desktop

vt normalize

A genetic variant can be represented in the Variant Call Format (VCF) in…

A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify…

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SWEEP
Desktop

SWEEP Sliding Window Extraction of Explicit Polymorphisms

Filters out false positives from a set of single nucleotide polymorphism (SNP)…

Filters out false positives from a set of single nucleotide polymorphism (SNP) calls. SWEEP uses the ubiquitous false-positive SNP calls and transforms them from a weakness to a strength by using…

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NGS-Bits
Desktop

NGS-Bits

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant…

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cyvcf2
Desktop

cyvcf2

Provides the ability to filter variants based upon variant annotation. cyvcf2…

Provides the ability to filter variants based upon variant annotation. cyvcf2 is a high-performance library that provides researchers with an intuitive Python interface for manipulating VCF files.…

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JfxNgs
Desktop

JfxNgs

Can read local files as long as they’ve been indexed with tabix or tribble.…

Can read local files as long as they’ve been indexed with tabix or tribble. JfxNgs is a computational package and a java-based user interface. It can also access the remote files if the hosting…

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bcftools
Desktop

bcftools

A statistical framework for calling SNPs, discovering somatic mutations,…

A statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data. BCFtools can…

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FMFilter
Desktop

FMFilter

Filters candidate variants according to the given criteria. FMFilter can handle…

Filters candidate variants according to the given criteria. FMFilter can handle compound heterozygous and de novo models properly. It offers options to make filtering according to genotype quality,…

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PileLine
Desktop

PileLine

Implements a flexible command-line toolkit providing specific support to the…

Implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of genomic position (GP) files produced by next generation sequencing…

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Htsjdk
Web

Htsjdk

Permits to get access to high-throughput sequencing data (HTS) formats. Htsjdk…

Permits to get access to high-throughput sequencing data (HTS) formats. Htsjdk does not support latest Variant Call Format Specification, for example VCFv4.3 and BCFv2.2. It can be useful to…

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VarAFT
Desktop

VarAFT Variant Annotation and Filter Tool

Annotates and filtrates variant files. VarAFT allows the comparison of several…

Annotates and filtrates variant files. VarAFT allows the comparison of several individuals and the collection of relevant information about the variations. It includes a coverage analysis module to…

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Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

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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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libGDF
Desktop

libGDF

Affords GDF’s (general dataformat for biosignals) implementation. libGDF…

Affords GDF’s (general dataformat for biosignals) implementation. libGDF provides a C++ version of the unify library data format for biomedical signals.

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pbcopper
Desktop

pbcopper

Comprises a repository of C++ applications. pbcopper is composed of six modules…

Comprises a repository of C++ applications. pbcopper is composed of six modules which provides information as well as command-line parsing, data types and data structures, JSON support, or…

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NCL
Desktop

NCL Nexus Class Library

Interprets data files created according to the NEXUS file format. The NCL is a…

Interprets data files created according to the NEXUS file format. The NCL is a C++ library that uses in phylogenetic systematics and molecular evolution.

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PyVCF
Desktop

PyVCF

Provides a way to read Variant Call Format files for Python.

Provides a way to read Variant Call Format files for Python.

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Pynnotator
Desktop

Pynnotator

Annotates Variant Call Formats (VCFs) generated from build GRCh37. Pynnotator…

Annotates Variant Call Formats (VCFs) generated from build GRCh37. Pynnotator was designed to annotate VCF files (Exomes or Genomes) from patients with Mendelian Disorders. The software uses…

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Pysam
Desktop

Pysam

Allows to read and manipulate SAM, BAM, VCF, and BCF files. Pysam focuses on…

Allows to read and manipulate SAM, BAM, VCF, and BCF files. Pysam focuses on SAM and BAM format because they permit to store efficiently large numbers of alignments.

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VCFmerge
Web
Desktop

VCFmerge

Combines VCF files of single samples into a single VCF file that contains all…

Combines VCF files of single samples into a single VCF file that contains all the samples. VCFmerge is a user friendly online interface based on tabix, bgzip, and vcftools.

vcfsubsample
Desktop

vcfsubsample

Helps about the Genome Wide Association (GWA) studies problem. Vcfsubsample…

Helps about the Genome Wide Association (GWA) studies problem. Vcfsubsample subsamples the data in order to "lock" the minor allele frequency (MAF) in the data set, i.e. all single…

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vcflib
Desktop

vcflib

A quick and extremely permissive method to read and write VCF files. vcflib…

A quick and extremely permissive method to read and write VCF files. vcflib provides a variety of functions for VCF manipulation: comparison, format conversion, filtering and subsetting, annotation,…

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