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vcf

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hail

hail-is / hail

Cloud-native genomic dataframes and batch computing

python bioinformatics gwas genomics genetics vcf software hail

Updated Oct 24, 2025
Python

samtools / htslib

C library for high-throughput sequencing data formats

bioinformatics ngs sam vcf bam htslib bcf cram

Updated Oct 23, 2025
C

tseemann / snippy

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Updated Jul 19, 2024
Perl

jeroendesloovere / vcard

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

php vcf vcard vcard-php

Updated Feb 2, 2024
PHP

Illumina / hap.py

Haplotype VCF comparison tools

bioinformatics genomics vcf vcf-comparison

Updated Dec 7, 2023
C++

brentp / cyvcf2

cython + htslib == fast VCF and BCF processing

bioinformatics genomics cython vcf htslib

Updated Oct 13, 2025
Cython

mskcc / vcf2maf

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

perl vcf maf vep isoforms

Updated Aug 2, 2025
Perl

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering

bioinformatics simulator vcf comparison bioconda structural-variations survivor

Updated Dec 1, 2023
C++

kcleal / gw

Genome browser and variant annotation

bam-files vcf genome-browser annotation-tool cram-files

Updated Aug 6, 2025
C++

brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

bioinformatics annotation genomics vcf

Updated Aug 30, 2025
Go

ACEnglish / truvari

Structural variant toolkit for VCFs

benchmarking data-science bioinformatics genomics sequencing vcf annotation-tool structural-variation vcf-comparison sv-merging

Updated Oct 11, 2025
Python

tariqdaouda / pyGeno

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

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

Updated Oct 7, 2025
Python

edgardomortiz / vcf2phylip

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

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

Updated Jul 7, 2023
Python

samtools / htsjdk

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

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

Updated Sep 26, 2025
Java

sigven / pcgr

Personal Cancer Genome Reporter (PCGR)

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

Updated Oct 7, 2025
R

lennart-k / rustical

a calendar server aiming to be simple, fast and passwordless

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

Updated Oct 21, 2025
Rust

bioSyntax / bioSyntax

Syntax highlighting for computational biology

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

Updated Mar 4, 2023
Shell

igordot / genomics

A collection of scripts and notes related to genomics and bioinformatics

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

Updated Oct 2, 2025
R

rutgerblom / SDDC.Lab

Automate deployment and configuration of nested VMware Software-Defined Data Center environments including solutions like vSphere, vSAN, NSX, vSphere Kubernetes Service, Avi Load Balancer, Aria Operations for Logs, VCF 9, VyOS, and ISC BIND.

vmware esxi vsphere ansible-playbooks vcf edge vyos bind alb vcenter nsx vsan sddc

Updated Sep 26, 2025
Jinja

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

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

Updated Sep 5, 2025
C

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