Top 53 vcf open source projects

Hap.py
Haplotype VCF comparison tools
Snippy
✂️ ⚡️ Rapid haploid variant calling and core genome alignment
✭ 245
perlvcf
Cyvcf2
cython + htslib == fast VCF and BCF processing
Vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
✭ 229
perlvcf
Htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
Survivor
Toolset for SV simulation, comparison and filtering
Pcgr
Personal Cancer Genome Reporter (PCGR)
Biosyntax
Syntax highlighting for computational biology
Vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Genomics
A collection of scripts and notes related to genomics and bioinformatics
Paragraph
Graph realignment tools for structural variants
✭ 92
vcf
Truvari
Structural variant toolkit for VCFs
Svtyper
Bayesian genotyper for structural variants
Mixerp.net.vcards
vCard Serializer and Parser for C#
Genozip
Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too
16gt
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Tiledb Vcf
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Gvanno
Generic germline variant annotation pipeline
Helmsman
highly-efficient & lightweight mutation signature matrix aggregation
Hail
Scalable genomic data analysis.
Htslib
C library for high-throughput sequencing data formats
Vcard
This vCard PHP library can easily parse or generate/export vCards as .vcf
✭ 333
vcf
Pygeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
VCF-kit
VCF-kit: Assorted utilities for the variant call format
23andme2vcf
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
telegram-json-to-vcf
Convert Telegram Contacts JSON File to VCF File
Ontologies
Home of the Genomic Feature and Variation Ontology (GFVO)
vcf2gwas
Python API for comprehensive GWAS analysis using GEMMA
SVCollector
Method to optimally select samples for validation and resequencing
jannovar
Annotation of VCF variants with functional impact and from databases (executable+library)
cutevariant
A standalone and free application to explore genetics variations from VCF file
ilus
A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
snps
tools for reading, writing, merging, and remapping SNPs
vcfstats
Powerful statistics for VCF files
2vcf
convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations
vcf stuff
📊Evaluating, filtering, comparing, and visualising VCF
CuteVCF
simple viewer for variant call format using htslib
laravel-vcard
A fluent builder class for vCard files.
vembrane
vembrane filters VCF records using python expressions
Variants2Neoantigen
A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
1-53 of 53 vcf projects