Projects in Awesome Lists tagged with vcf

https://github.com/hail-is/hail

Cloud-native genomic dataframes and batch computing

bioinformatics genetics genomics gwas hail python software vcf

Last synced: 13 May 2025

https://github.com/samtools/htslib

C library for high-throughput sequencing data formats

bam bcf bioinformatics cram htslib ngs sam vcf

Last synced: 29 Dec 2025

https://github.com/jeroendesloovere/vcard

This vCard PHP library can easily parse or generate/export vCards as .vcf

php vcard vcard-php vcf

Last synced: 14 May 2025

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/lennart-k/rustical

a calendar server aiming to be simple, fast and passwordless

address-book addressbook axum caldav caldav-server calendar carddav dav dav-push icalendar ics oidc rust vcf

Last synced: 22 May 2026

https://github.com/illumina/hap.py

Haplotype VCF comparison tools

bioinformatics genomics vcf vcf-comparison

Last synced: 04 Apr 2025

https://github.com/brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

bioinformatics cython genomics htslib vcf

Last synced: 27 Jan 2026

https://github.com/mskcc/vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

isoforms maf perl vcf vep

Last synced: 15 May 2025

https://github.com/fritzsedlazeck/survivor

Toolset for SV simulation, comparison and filtering

bioconda bioinformatics comparison simulator structural-variations survivor vcf

Last synced: 05 Apr 2025

https://github.com/brentp/vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

annotation bioinformatics genomics vcf

Last synced: 12 Apr 2025

https://github.com/tariqdaouda/pygeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 09 Oct 2025

https://github.com/tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 30 Mar 2025

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 2025

https://github.com/sigven/pcgr

Personal Cancer Genome Reporter (PCGR)

annotation-framework annotation-tool cancer cancer-genomics cancer-variants clinical copy-number-variation interpreter oncology-data precision-cancer-medicine precision-oncology reporting-engine snvs somatic therapeutic-targets tumor variant-interpretation vcf

Last synced: 27 Feb 2026

https://github.com/bioSyntax/bioSyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 05 May 2025

https://github.com/biosyntax/biosyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 07 Apr 2025

https://github.com/edgardomortiz/vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

alignment binary convert-snps diploid fasta haploid nexus outgroup phylip phylip-matrix phylogenetic-analysis phylogenetics polyploid snapp snps vcf vcf-files vcf-format

Last synced: 28 Feb 2026

https://github.com/igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

bioinformatics dna fast5 fasta fastq genomics gtf illumina nanopore science sequencing vcf workflow

Last synced: 21 Jan 2026

https://github.com/helicalAI/helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

artificial-intelligence bioinformatics biology deep-learning dna-sequences evo2 foundation-models gene-expression geneformer helixmrna pre-trained-model pre-training rna rna-seq rnaseq scgpt transcriptformer transformer uce vcf

Last synced: 27 May 2026

https://github.com/divonlan/genozip

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

23andme bam bgzip bwa compression cram fasta fastq genomics gvf gzip sam samtools vcf

Last synced: 13 May 2026

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/illumina/paragraph

Graph realignment tools for structural variants

genotyping htslib structural-variation variant-calling vcf

Last synced: 09 Jul 2025

https://github.com/aehrc/variantspark

machine learning for genomic variants

association-studies aws bioinformatics databricks emr genome gwas notebook random-forest variant-spark variantspark vcf

Last synced: 06 Apr 2025

https://github.com/brentp/peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

ancestry bioinformatics genomics genotype pedigree vcf

Last synced: 07 Apr 2025

https://github.com/apriha/snps

tools for reading, writing, generating, merging, and remapping SNPs

bioinformatics chromosomes dna snps vcf

Last synced: 28 Jan 2026

https://github.com/bihealth/vcfpy

Python 3 library with good support for both reading and writing VCF

bioinformatics file-format parsing vcf writing

Last synced: 12 Feb 2026

https://github.com/labsquare/cutevariant

A standalone and free application to explore genetics variations from VCF file

genetics gui pyside2 python3 variant-call-format vcf

Last synced: 07 Apr 2025

https://github.com/arrogantrobot/23andme2vcf

convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf

23andme ancestry annotations perl vcf

Last synced: 11 Jan 2026

https://github.com/jhermsmeier/node-vcf

A not so forgiving vCard / vcf parser

format jcard parser vcard vcf

Last synced: 05 Apr 2025

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/chasewnelson/snpgenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

diversity-measurement dnds dnds-estimation evolution evolutionary-parameters fasta-sequences molecular-evolution natural-selection nei-gojobori next-generation-sequencing nucleotide nucleotide-diversity perl population-genetics sequence-analysis snp-report substitution-rate vcf vcf-files

Last synced: 23 Mar 2025

https://github.com/chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

2bit bam bcf bed bigwig bioinformatics clojure cram fasta fastq genomics gff sam vcf wig

Last synced: 16 May 2025

https://github.com/polykit/polykit-x-monosynth

The Polykit X1 is a DIY semi-modular, analog, patchable synthesizer

adsr analog diy kicad modular oscillator pcb schematics synth synthesizer vca vcf wavefolder

Last synced: 23 Feb 2026

https://github.com/mixerp/mixerp.net.vcards

vCard Serializer and Parser for C#

csharp dotnet vcard vcf

Last synced: 13 May 2025

https://github.com/pwwang/vcfstats

Powerful statistics for VCF files

vcf vcf-files vcfstats

Last synced: 22 Sep 2025

https://github.com/sigven/cpsr

Cancer Predisposition Sequencing Reporter (CPSR)

acmg cancer cancer-genomics cancer-predisposition cancer-predisposition-report cancer-research docker genomics-england-panelapp germline-variants inherited pathogenic-loci pathogenic-variants pathogenicity predisposition report-generator reporting-tool vcf workflow-engine

Last synced: 27 Feb 2026

https://github.com/kelseykm/vcard4

An RFC 6350 compliant JavaScript library (with TypeScript type declarations) for generating and parsing version 4.0 vCards. Can also generate RFC 6351 compliant XML vCards and RFC 7095 compliant jCards.

jcard rfc6350 rfc6351 rfc7095 vcard vcard-parser vcf xml-card

Last synced: 30 Apr 2025

https://github.com/varfish-org/varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research

genetics varfish variant-filtration variant-prioritization vcf

Last synced: 10 Mar 2026

https://github.com/astrotomic/laravel-vcard

A fluent builder class for vCard files.

contact contacts laravel vcard vcf

Last synced: 24 Apr 2025

https://github.com/brentp/hts-nim-tools

useful command-line tools written to showcase hts-nim

bam bioinformatics genomics nim nim-lang vcf vcf-filtering

Last synced: 09 Aug 2025

https://github.com/plantimals/2vcf

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

23andme ancestry annotations dbsnp vcf

Last synced: 14 Jan 2026

https://github.com/sbslee/fuc

Frequently used commands in bioinformatics

api bam bed bioinformatics cli cram fasta fastq gff gtf maf sam vcf visualization

Last synced: 06 Apr 2025

https://github.com/gorpipe/gor

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

bioinformatics genetics genomics gor gorpipe gwas java open-source python scala software spark vcf

Last synced: 02 Apr 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/rillke/contact-conversion-wizard

Programm um auf einfache Weise Kontaktlisten zwischen verschiedenen Programmen/Geräten zu konvertieren

aastra address-book auerswald converter csharp csv fritz-box gigaset google-contacts grandstream gui snom vcard vcf

Last synced: 16 Jun 2025

https://github.com/jhbruhn/eurorack

Eurorack Module Designs, often based on popular designs but modified to be even more...escalative.

analog digital eurorack mcp4922 mixer stereo stereo-mixer stm32 synthesizer vca vcf

Last synced: 10 Jun 2025

https://github.com/zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

annotation bcf bgen meta-analysis next-generation-sequencing plink sequencing tabix vcf workflow

Last synced: 18 Feb 2026

https://github.com/orangeSi/GSSplayground

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

bam bioinformatics comparative-genomics crosslink depth genecluster genome-viewer genomes igv-like indel long-reads read-mapping snp structure-variation sv svg synteny transcriptomics vcf visualization

Last synced: 18 Nov 2025

https://github.com/labsquare/cutevcf

simple viewer for variant call format using htslib

bioinformatics genomics gui qt5 variants vcf

Last synced: 14 Aug 2025

https://github.com/shixiangwang/variants2neoantigen

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

cancer-genomics maf neoantigen vcf

Last synced: 12 Apr 2025

https://github.com/bolorundurowb/vcardlib

📇 A .NET standard library for reading and writing vCard files

c-sharp library vcard vcf

Last synced: 27 Dec 2025

https://github.com/fritzsedlazeck/svcollector

Method to optimally select samples for validation and resequencing

bioinformatics long-reads ngs ngstools structural-variation vcf

Last synced: 08 Jul 2025

https://github.com/aquaskyline/16gt

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

bioinformatics call-variants computational-biology genome indels snps vcf

Last synced: 21 Mar 2025

https://github.com/shujiahuang/cmdbtools

Command line tools for CMDB varaints browser

bioinformatics chinese-genome-database chinese-millionome-database cmdb database genomics-api variants vcf

Last synced: 06 Apr 2025

https://github.com/ngthomas/microhaplot

microhaplotype visualizer and analyzer

amplicon-sequencing microhaplot-shiny shiny vcf

Last synced: 22 Oct 2025

https://github.com/openmendel/vcftools.jl

Julia utilities for handling VCF files

julia vcf

Last synced: 27 Oct 2025

https://github.com/varfish-org/hgvs-rs

A port of biocommons/hgvs to the Rust programming language

genetics varfish variant-filtration variant-prioritization vcf

Last synced: 11 Apr 2026

https://github.com/schorschii/quicksync4linux

Upload/download files, backup/sync contacts and communicate with your Gigaset devices

at gigaset obex phonebook quicksync serial vcf

Last synced: 24 Jul 2025

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

The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049

bioinformatics fastr htslib population-genetics population-genomics rstats vcf vcf-data visulization

Last synced: 22 Jun 2025

https://github.com/polykit/vcf-3350-8

CEM3350/AS3350 based 8 channel VCF

as3350 cem3350 filter kicad pcb polysynth schematics synthesizer vcf

Last synced: 05 Jan 2026

https://github.com/lifeomic/spark-vcf

Spark VCF data source implementation for Dataframes

dataframe genomics genotype lifeomic spark spark-sql team-clinical-intelligence variants vcf vcf-files

Last synced: 13 Sep 2025

https://github.com/sauternic/vcard-to-csv

Makes vCard (.vcf) data readable

csv html javascript parser readable vcard vcard-parser vcf

Last synced: 12 May 2025

https://github.com/isinaltinkaya/vcfgl

Genotype likelihood simulator for VCF/BCF files

genotype-likelihoods msprime simulation tskit vcf vcf-files

Last synced: 21 Feb 2026

https://github.com/rasmushenningsson/variantcallformat.jl

Read and write VCF and BCF files

bcf bioinformatics genetics julia vcf vcf-files

Last synced: 16 Mar 2026

https://github.com/fritzsedlazeck/survivor_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)

annotation structural-variations svs vcf

Last synced: 17 Feb 2026

https://github.com/bigbio/py-pgatk

Python tools for proteogenomics analysis toolkit

ensembl mass-spectrometry proteogenomics proteogenomics-analysis-toolkit proteomics python vcf

Last synced: 17 Jan 2026

https://github.com/folkerkinzel/vcards

.NET library for reading, writing, and converting VCF files that comply with vCard standards 2.1, 3.0 and 4.0

csharp dotnet vcard vcf

Last synced: 29 Dec 2025

https://github.com/HelixGenomics/Genomic-Agent-Discovery

AI agents that collaborate to analyze your DNA. 12 public databases, real-time dashboard, runs 100% locally. Drop in your 23andMe, AncestryDNA, or VCF file.

23andme ai-agents ancestrydna bioinformatics claude clinvar dna genetic-testing genomics gwas llm mcp model-context-protocol multi-agent personal-genomics pharmacogenomics precision-medicine privacy snp vcf

Last synced: 19 Apr 2026

https://github.com/edawson/svaha

Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]

gfa graph variation-graph vcf

Last synced: 24 Apr 2025

https://github.com/aehrc/tribes

Finding cryptic relationships to boost disease gene detection

estimate-relationships ibd-segments pipeline vcf

Last synced: 12 Apr 2025

https://github.com/lindenb/hts-rdf

Managing sequencing data with RDF

bam bioinformatics data-management ontology rdf sparql tutorial vcf

Last synced: 13 Mar 2026

https://github.com/helixgenomics/genomic-agent-discovery

AI agents that collaborate to analyze your DNA. 12 public databases, real-time dashboard, runs 100% locally. Drop in your 23andMe, AncestryDNA, or VCF file.

23andme ai-agents ancestrydna bioinformatics claude clinvar dna genetic-testing genomics gwas llm mcp model-context-protocol multi-agent personal-genomics pharmacogenomics precision-medicine privacy snp vcf

Last synced: 05 Apr 2026

https://github.com/pimalaya/cardamum

CLI to manage contacts

addressbook cardamum carddav cli client contacts pim pimalaya vcard vcf webdav

Last synced: 02 Aug 2025

https://github.com/poisonalien/varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.

converts-varscan-somatic copynumber segmentation somatic-variants varscan vcf

Last synced: 24 Jul 2025

https://github.com/orangesi/tinypandas

easy-to-use data structures and data analysis tools ( still be in draft, inspired by Python Pandas )

crystal crystal-lang csv dataframe pandas-python vcf

Last synced: 20 Aug 2025

https://github.com/jslfree080/bamscope

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

bam bam-files bioinformatics genomics genomics-visualization samtools vcf

Last synced: 18 Nov 2025

https://github.com/brentp/xvcf-rs

VCF/BCF [un]compressed [un]indexed

genomics vcf

Last synced: 29 Oct 2025

https://github.com/samuelnicaise/variantconvert

A customizable genetic variants file format converter.

bioinformatics conversion converter file genetics ngs tsv variants vcf

Last synced: 30 Apr 2025

https://github.com/hirbodbehnam/telegramtovcf

Export your Telegram contacts as VCF

telegram vcf

Last synced: 26 Mar 2025

https://github.com/animesh-chouhan/vcf-creator

Generate vCard file from CSV

csv-to-vcf python vcf vcf-converter

Last synced: 05 Apr 2025

https://github.com/chrovis/varity

Variant translation library for Clojure

bioinformatics clojure hgvs liftover vcf

Last synced: 03 May 2025

https://github.com/vmware/terraform-vcf-toolkit

The VMware Cloud Foundation Terraform Toolkit utilizes Terraform to build customer-ready consumable infrastructure using the principles of infrastructure as code.

terraform vcf vmware

Last synced: 04 Apr 2026