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Projects in Awesome Lists tagged with variant-calling

A curated list of projects in awesome lists tagged with variant-calling .

https://github.com/tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

allmaps assembly bioinformatics blast comparative-genomics genetic-maps genome-sequencing genomics sequence-alignments synteny variant-calling

Last synced: 14 May 2025

https://github.com/ekg/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 20 Apr 2025

https://github.com/vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 25 Feb 2026

https://github.com/tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

bacteria bioinformatics fastq-analysis genomics haploid indel-discovery snps variant-calling vcf

Last synced: 12 Apr 2025

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 12 Feb 2026

https://github.com/HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

computational-biology deep-learning genomics illumina long-reads nanopore ont-data ont-models pacbio variant-calling variant-detection

Last synced: 11 Jun 2026

https://github.com/hku-bal/clair3

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

computational-biology deep-learning genomics illumina long-reads nanopore ont-data ont-models pacbio variant-calling variant-detection

Last synced: 27 Apr 2026

https://github.com/nanoporetech/megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

basecalling epigenetics guppy variant-calling

Last synced: 29 Mar 2025

https://github.com/aquaskyline/clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

bioinformatics computational-biology deep-learning variant-calling

Last synced: 13 Apr 2025

https://github.com/sequana/sequana

Sequana: a set of Snakemake NGS pipelines

coverage de-novo ngs pacbio rna-seq sequanix snakemake taxonomy variant-calling

Last synced: 17 Jan 2026

https://github.com/illumina/paragraph

Graph realignment tools for structural variants

genotyping htslib structural-variation variant-calling vcf

Last synced: 09 Jul 2025

https://github.com/Illumina/paragraph

Graph realignment tools for structural variants

genotyping htslib structural-variation variant-calling vcf

Last synced: 10 May 2025

https://github.com/shujiahuang/ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

bioinformatics bioinformatics-pipeline pipeline variant-calling whole-genome-sequencing workflow-management

Last synced: 12 Apr 2025

https://github.com/tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

bacteria denovo-assembly fastq genotyping phylogenomics public-health report resistome variant-calling virulome

Last synced: 12 Apr 2025

https://github.com/mcveanlab/mccortex

De novo genome assembly and multisample variant calling

contigs cortex de-bruijn-graphs genome-analysis genome-assembly genome-graph genomics kmer variant-calling

Last synced: 17 Dec 2025

https://github.com/lh3/fermikit

De novo assembly based variant calling pipeline for Illumina short reads

bioinformatics denovo-assembly genomics variant-calling

Last synced: 13 Feb 2026

https://github.com/tiledb-inc/tiledb-vcf

Efficient variant-call data storage and retrieval library using the TileDB storage library.

bioinformatics data-science genomics gwas python spark tiledb variant-calling vcf

Last synced: 05 Apr 2025

https://github.com/lh3/minipileup

Simple pileup-based variant caller

bioinformatics variant-calling

Last synced: 09 Apr 2025

https://github.com/karel-brinda/ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

bioinformatics consensus ngs online-algorithms variant-calling

Last synced: 04 Mar 2025

https://github.com/nvidia/variantworks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

deep-learning genomics polishing variant-calling

Last synced: 06 Mar 2026

https://github.com/clinical-genomics/balsamic

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

bioinformatics genomics snakemake-workflows somatic-mutations variant-calling

Last synced: 15 Aug 2025

https://github.com/genomic-medicine-sweden/nallo

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

gms long-read-sequencing nanopore pacbio variant-calling

Last synced: 17 Jan 2026

https://github.com/brentp/indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

genome-assembly genomics k-mer-counting local-assembly nim-lang variant-calling vcf

Last synced: 22 Jun 2025

https://github.com/sib-swiss/ngs-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

course gatk ngs ngs-analysis teaching training tutorial variant-calling

Last synced: 14 Apr 2025

https://github.com/mcvickerlab/varca

Use an ensemble of variant callers to call variants from ATAC-seq data

atac-seq-data machine-learning random-forest snakemake variant-calling

Last synced: 01 Apr 2026

https://github.com/aryarm/varca

Use an ensemble of variant callers to call variants from ATAC-seq data

atac-seq-data machine-learning random-forest snakemake variant-calling

Last synced: 11 Apr 2025

https://github.com/mbhall88/nanovarbench

Evaluating Nanopore-based bacterial variant calling

bacteria benchmark bioinformatics illumina microbial-genomics nanopore variant-calling

Last synced: 03 Mar 2026

https://github.com/pdimens/harpy

Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!

bioinformatics haplotype linked-reads pipeline sequencing variant-calling

Last synced: 03 Feb 2026

https://github.com/nbisweden/workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

bioinformatics ngs-analysis rnaseq unix-shell variant-calling

Last synced: 06 Oct 2025

https://github.com/tobiasrausch/nrex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling

Last synced: 10 Jul 2025

https://github.com/mbhall88/tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

bioinformatics drug-resistance-prediction genomics mycobacterium-tuberculosis nanopore variant-calling

Last synced: 01 Mar 2026

https://github.com/fedarko/strainflye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

bioinformatics metagenomics phasing variant-calling

Last synced: 19 Aug 2025

https://github.com/sanger-tol/variantcalling

Nextflow DSL2 pipeline to call variants on long read alignment.

alignment genomics nextflow pipeline variant-calling workflow

Last synced: 17 Jan 2026

https://github.com/vccri/dv-trio

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

father-mother-child mendelian-genetics variant-calling variants

Last synced: 10 Apr 2025

https://github.com/inmegen/pipelines_inmegen

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

bioinformatics differential-expression dockerfile genomic-data-analysis nextflow-pipeline rnaseq-analysis somatic-variants transcriptome-analysis variant-calling

Last synced: 08 Apr 2026

https://github.com/dmnfarrell/snipgenie

command line and desktop tool for microbial variant calling

bioinformatics genomics ngs-pipeline pyqt5 pyside2 python variant-calling

Last synced: 15 Apr 2025

https://github.com/cdcgov/nchhstp-dtbe-varpipe-wgs

This repository contains an analysis pipeline developed to characterize WGS output

bioinformatics bioinformatics-pipeline genomics pipeline variant-annotations variant-calling

Last synced: 13 Apr 2026

https://github.com/zilong-li/basevarc

The repo was not under development. Check out angsd toolkit for low depth data analyses.

bioinformatics-tool low-coverage-sequencing population-genetics variant-calling

Last synced: 01 Aug 2025

https://github.com/brwnj/freebayes-nf

a better freebayes-parallel

freebayes parallel-computing variant-calling

Last synced: 16 Oct 2025

https://github.com/sateeshperi/nextflow_varcal

Nextflow Tutorial - Variant Calling Edition

data-carpentry nextflow nf-core variant-calling

Last synced: 22 Aug 2025

https://github.com/aprilweilab/picovcf

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

c-plus-plus comp-bio header-only header-only-library variant-calling vcf

Last synced: 25 Apr 2025

https://github.com/tobiasrausch/covid19

SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing

consensus covid19 covid19-analysis sars-cov-2 variant-calling whole-genome-sequencing

Last synced: 13 Apr 2025

https://github.com/tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

cancer-genomics k-mer pan-genome rare-disease reference-free sequencing variant-calling

Last synced: 13 Apr 2025

https://github.com/clintval/vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.

bioinformatics rust variant-calling

Last synced: 27 Feb 2026

https://github.com/fulcrumgenomics/twistcgp

Nextflow pipeline for Twist Comprehensive Genomic Profiling (CGP) panel analysis

bioinformatics genomics nextflow nf-core oncology variant-calling

Last synced: 08 May 2026

https://github.com/aprilweilab/pyigd

Python-only parser for Indexable Genotype Data (IGD) format.

comp-bio python variant-calling

Last synced: 25 Apr 2025

https://github.com/combat-tb/vcf2neo

A tool to import SnpEff annotated files to a Neo4j Graph database

graph-database neo4j-database py2neo snpeff tuberculosis variant-calling

Last synced: 19 Apr 2025

https://github.com/rki-mf1/cievad

A tool suite for a simple, streamlined and rapid evaluation of variant callsets

benchmarking bioinformatics genomics indels nextflow ngs oxford-nanopore snps variant-calling

Last synced: 17 Jan 2026

https://github.com/ghga-de/nf-platypusindelcalling

This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ

annotation annotations dkfz ghga indel-calling nextflow nextflow-pipeline odcf pipeline platypus somatic-mutations somatic-variants variant-calling workflow

Last synced: 04 Apr 2026

https://github.com/georgiesamaha/fq2vcf

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

bam bioinformatics gatk genomics indels mapping ngs pipeline snps variant-calling vcf

Last synced: 15 Mar 2025

https://github.com/k8hertweck/bacterialgenomics

example genomics workflow for student training

bacteria genome-assembly genomics variant-calling

Last synced: 10 May 2026

https://github.com/oicr-gsi/delly

Delly workflow produces a set of vcf files with different types of structural variant calls

structural-variation variant-calling workflow

Last synced: 03 Apr 2026

https://github.com/mpusp/snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

bowtie2 bwa-mem2 genomics mapping next-generation-sequencing snakemake snakemake-workflow star-alignment variant-calling

Last synced: 11 Mar 2026

https://github.com/solida-core/diva

DiVA (DNA Variant Analysis) is a pipeline for Next-Generation Sequencing Exome data anlysis

bioinformatics genomics snakemake variant-annotations variant-calling workflow

Last synced: 12 Apr 2025

https://github.com/sydney-informatics-hub/germlineshortv_biovalidation

Workflow for biological validation of germline SNP and indel variant datasets.

germline indel snp validation variant-analysis variant-calling wgs wholegenomesequencing

Last synced: 15 Mar 2025

https://github.com/tdayris/fair_gatk_mutect2

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

fair gatk-bestpractices mutect2 reproducible-workflows snakemake snakemake-workflow variant-calling

Last synced: 16 Jan 2026

https://github.com/oicr-gsi/sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

fingerprinting genotyping qc reporting variant-calling workflow

Last synced: 03 Apr 2026

https://github.com/oicr-gsi/freec

freec workflow - call CNV on your tumor wih optional normal

analysis cnv variant-calling workflow

Last synced: 03 Apr 2026

https://github.com/giatraskon/chromosome11-variantcalling-gatk

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

1000genomes bam bcftools bioinformatics bwa exome-sequencing gatk gatk4-haplotypecaller genome-analysis haplotypecaller human-genome indels population-genetics reference-genome samtools snpeff snps variant-annotation variant-calling vcf

Last synced: 29 Jun 2025

https://github.com/meeranhussain/population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

genome-analysis ngs ngs-analysis population population-genomics rprogramming snakemake-workflow variant-calling whole

Last synced: 25 Feb 2025

https://github.com/brendancsmith/vcf-isec

A simple python implementation of Variant Call Format intersection and complements for identifying genetic mutations

bioinformatics genome variant-call-format variant-calling

Last synced: 20 Apr 2026

https://github.com/mbhall88/qmrl-slides

Slides for presentation to the Queensland Mycobacterium Reference Laboratory 24/02/2022

bioinformatics drug-resistance-prediction genomics nanopore slides transmission-clustering tuberculosis variant-calling

Last synced: 18 Mar 2025

https://github.com/leooojr/divv

Differential Investigation of Variability in Variants

bioinformatics python variant-analysis variant-calling variants vcf vcf-comparison

Last synced: 17 May 2026

https://github.com/alexcoppe/vcf_to_tsv

Transforms a VCF (variant call format) file to a tab-separated values (.tsv) one

bioinformatics cpp genomics mutations variant-calling vcf

Last synced: 13 Oct 2025

https://github.com/leooojr/vusion

Merge and reconcile VCF files

bioinformatics biology ngs python variant-calling variants vcf

Last synced: 14 Oct 2025

https://github.com/gauravcodepro/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants

Last synced: 19 Jul 2025

https://github.com/berntpopp/variant-linker

🧬 Powerful CLI tool and JavaScript library for genetic variant annotation using Ensembl APIs. Supports SNVs, CNVs, VCF files, inheritance analysis, batch processing, and genome assembly liftover.

batch-processing bioinformatics cli-tool cnv computational-biology ensembl genetic-variants genetics genome-assembly genomics inheritance-analysis javascript-library liftover medical-genetics nodejs snp variant-annotation variant-calling vcf vep

Last synced: 23 Jan 2026

https://github.com/carpentries-israel/2024-10-29-wis

Public site for Data Carpentry Genomics workshop at Weizmann Institute of Science, October 2024

bash bioinformatics bioinformatics-workshop carpentries data-carpentry genomics genomics-workshop r variant-calling

Last synced: 30 Jan 2026

https://github.com/stevekm/mutect2_target_chunking

demo pipeline for testing different data chunking methods for MuTect2

mutect2 nextflow variant-calling

Last synced: 30 Jan 2026

https://github.com/multimeric/improvar

A python script for generating sample VCF data based on a template VCF

bioinformatics variant-calling vcf

Last synced: 17 Jun 2025

https://github.com/thanhleviet/dengue-wgs

A Custom Variant Calling Pipeline for Dengue WGS (BWA + GATK + Lofreq) using nextflow and docker

bioinformatics-pipeline dengue nextflow variant-calling

Last synced: 26 Feb 2026

https://github.com/tmsincomb/deepvcf

Variant Calling with Deep Learning for Prokaryotic genomes using TensorFlow. Adds (0 <= P(Variant) <= 1) to VCF files under INFO as abbreviated "ACC=".

deep-learning deeplearning prokaryotes prokaryotic-genomes variant-call-format variant-calling vcf

Last synced: 06 Mar 2025