vcf
There are 472 repositories under vcf topic.
hail-is/hail
Cloud-native genomic dataframes and batch computing
samtools/htslib
C library for high-throughput sequencing data formats
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
jeroendesloovere/vcard
This vCard PHP library can easily parse or generate/export vCards as .vcf
Illumina/hap.py
Haplotype VCF comparison tools
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
mskcc/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
fritzsedlazeck/SURVIVOR
Toolset for SV simulation, comparison and filtering
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
ACEnglish/truvari
Structural variant toolkit for VCFs
kcleal/gw
Genome browser and variant annotation
tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
edgardomortiz/vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
samtools/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
bioSyntax/bioSyntax
Syntax highlighting for computational biology
sigven/pcgr
Personal Cancer Genome Reporter (PCGR)
igordot/genomics
A collection of scripts and notes related to genomics and bioinformatics
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
Illumina/paragraph
Graph realignment tools for structural variants
helicalAI/helical
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
aehrc/VariantSpark
machine learning for genomic variants
davetang/learning_vcf_file
Learning the Variant Call Format
brentp/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
PharmGKB/PharmCAT
The Pharmacogenomic Clinical Annotation Tool
AndersenLab/VCF-kit
VCF-kit: Assorted utilities for the variant call format
hall-lab/svtyper
Bayesian genotyper for structural variants
chasewnelson/SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
apriha/snps
tools for reading, writing, merging, and remapping SNPs
bihealth/vcfpy
Python 3 library with good support for both reading and writing VCF
starskyzheng/panpop
Application of pan-genome for population
labsquare/cutevariant
A standalone and free application to explore genetics variations from VCF file
arrogantrobot/23andme2vcf
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
frankvogt/vcf2gwas
Python API for comprehensive GWAS analysis using GEMMA
TileDB-Inc/TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
chrovis/cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
TimD1/vcfdist
vcfdist: Accurately benchmarking phased variant calls