hail-is/hail

Cloud-native genomic dataframes and batch computing

Language: Python - Size: 118 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 925 - Forks: 235

samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 12.4 MB - Last synced: about 14 hours ago - Pushed: 1 day ago - Stars: 775 - Forks: 446

jeroendesloovere/vcard

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

Language: PHP - Size: 470 KB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 492 - Forks: 186

tseemann/snippy

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

Language: Perl - Size: 124 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 408 - Forks: 111

Illumina/hap.py

Haplotype VCF comparison tools

Language: C++ - Size: 177 MB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 388 - Forks: 119

brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

Language: Cython - Size: 14.7 MB - Last synced: 2 days ago - Pushed: 2 months ago - Stars: 357 - Forks: 71

brentp/vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

Language: Go - Size: 37.1 MB - Last synced: 2 days ago - Pushed: 6 months ago - Stars: 348 - Forks: 55

mskcc/vcf2maf

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

Language: Perl - Size: 15.8 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 336 - Forks: 216

tariqdaouda/pyGeno

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

Language: Python - Size: 10.6 MB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 307 - Forks: 52

fritzsedlazeck/SURVIVOR

Toolset for SV simulation, comparison and filtering

Language: C++ - Size: 20.1 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 299 - Forks: 43

ACEnglish/truvari

Structural variant toolkit for VCFs

Language: Python - Size: 98.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 291 - Forks: 48

samtools/htsjdk

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

Language: Java - Size: 109 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 272 - Forks: 244

bioSyntax/bioSyntax

Syntax highlighting for computational biology

Language: Shell - Size: 2.53 MB - Last synced: 2 days ago - Pushed: about 1 year ago - Stars: 247 - Forks: 30

sigven/pcgr

Personal Cancer Genome Reporter (PCGR)

Language: R - Size: 70.8 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 236 - Forks: 49

edgardomortiz/vcf2phylip

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

Language: Python - Size: 136 KB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 232 - Forks: 80

igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

Language: R - Size: 241 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 182 - Forks: 51

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

Language: C - Size: 966 MB - Last synced: 2 days ago - Pushed: 20 days ago - Stars: 149 - Forks: 10

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

aehrc/VariantSpark

machine learning for genomic variants

Language: JavaScript - Size: 74.5 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 138 - Forks: 44

kcleal/gw

Genome browser and variant annotation

Language: C++ - Size: 16.1 MB - Last synced: about 19 hours ago - Pushed: about 22 hours ago - Stars: 137 - Forks: 5

davetang/learning_vcf_file

Learning the Variant Call Format

Language: Perl - Size: 42.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 135 - Forks: 40

brentp/peddy

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

Language: Jupyter Notebook - Size: 39.3 MB - Last synced: 8 days ago - Pushed: almost 3 years ago - Stars: 127 - Forks: 38

AndersenLab/VCF-kit

VCF-kit: Assorted utilities for the variant call format

Language: Python - Size: 10.9 MB - Last synced: 2 days ago - Pushed: 8 months ago - Stars: 119 - Forks: 25

hall-lab/svtyper

Bayesian genotyper for structural variants

Language: Python - Size: 2.21 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 119 - Forks: 53

jhermsmeier/node-vcf

A not so forgiving vCard / vcf parser

Language: JavaScript - Size: 218 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 96 - Forks: 36

arrogantrobot/23andme2vcf

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

Language: Perl - Size: 29.1 MB - Last synced: 18 days ago - Pushed: over 4 years ago - Stars: 94 - Forks: 30

chasewnelson/SNPGenie

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

Language: Perl - Size: 876 KB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 92 - Forks: 37

apriha/snps

tools for reading, writing, merging, and remapping SNPs

Language: Python - Size: 2.06 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 91 - Forks: 18

labsquare/cutevariant

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

Language: Python - Size: 69.2 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 89 - Forks: 20

chrovis/cljam

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

Language: Clojure - Size: 35.1 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 88 - Forks: 12

bihealth/vcfpy

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

Language: Python - Size: 1.25 MB - Last synced: 8 days ago - Pushed: about 2 months ago - Stars: 84 - Forks: 18

TileDB-Inc/TileDB-VCF

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

Language: C++ - Size: 33 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 79 - Forks: 13

Moduland/csv2vcf

🔧 Simple script in python to convert CSV files to VCF

Language: Python - Size: 810 KB - Last synced: 28 days ago - Pushed: about 2 months ago - Stars: 70 - Forks: 23

mixerp/MixERP.Net.VCards

vCard Serializer and Parser for C#

Language: C# - Size: 294 KB - Last synced: 11 days ago - Pushed: over 4 years ago - Stars: 70 - Forks: 41

BernieO/calcardbackup 📦

calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup

Size: 942 KB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 69 - Forks: 5

starskyzheng/panpop

Application of pan-genome for population

Language: Perl - Size: 62 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 68 - Forks: 7

TimD1/vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language: C++ - Size: 61.4 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 67 - Forks: 5

frankvogt/vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA

Language: Python - Size: 27 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 63 - Forks: 25

polykit/polykit-x-monosynth

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

Size: 8.42 MB - Last synced: 21 days ago - Pushed: 5 months ago - Stars: 58 - Forks: 3

vembrane/vembrane

vembrane filters VCF records using python expressions

Language: Python - Size: 18.4 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 56 - Forks: 5

pwwang/vcfstats

Powerful statistics for VCF files

Language: Python - Size: 1.69 MB - Last synced: 14 days ago - Pushed: 7 months ago - Stars: 54 - Forks: 17

charite/jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)

Language: Java - Size: 23.6 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 54 - Forks: 37

sigven/cpsr

Cancer Predisposition Sequencing Reporter (CPSR)

Language: R - Size: 18.8 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 52 - Forks: 12

brentp/hts-nim-tools

useful command-line tools written to showcase hts-nim

Language: Nim - Size: 11.7 KB - Last synced: 9 days ago - Pushed: over 3 years ago - Stars: 48 - Forks: 6

plantimals/2vcf

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

Language: Go - Size: 25.2 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 47 - Forks: 4

sigven/gvanno

Generic human DNA variant annotation pipeline

Language: Python - Size: 13.7 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 44 - Forks: 11

sbslee/fuc

Frequently used commands in bioinformatics

Language: Python - Size: 1.17 MB - Last synced: 8 days ago - Pushed: 8 months ago - Stars: 44 - Forks: 5

Astrotomic/laravel-vcard

A fluent builder class for vCard files.

Language: PHP - Size: 199 KB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 44 - Forks: 14

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.

Language: JavaScript - Size: 5.96 MB - Last synced: 4 days ago - Pushed: 6 months ago - Stars: 43 - Forks: 6

everestial/VCF-Simplify

A python parser to simplify and build the VCF (Variant Call Format).

Language: Python - Size: 19.9 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 43 - Forks: 12

s-nikravesh/telegram-json-to-vcf

Convert Telegram Contacts JSON File to VCF File

Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 42 - Forks: 6

sigven/vcf2tsvpy

Genomic VCF to tab-separated values

Language: Python - Size: 59.6 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 41 - Forks: 11

varfish-org/varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research

Language: Python - Size: 54.7 MB - Last synced: 17 days ago - Pushed: 19 days ago - Stars: 40 - Forks: 11

brentp/indelope

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

Language: Nim - Size: 133 KB - Last synced: 9 days ago - Pushed: over 6 years ago - Stars: 39 - Forks: 1

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.

Language: Java - Size: 13.1 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 38 - Forks: 13

MRCIEU/gwas2vcf

Convert GWAS summary statistics to VCF

Language: Python - Size: 5.42 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 37 - Forks: 15

elimuinformatics/vcf2fhir

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration

Language: Python - Size: 2.1 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 36 - Forks: 23

labsquare/CuteVCF

simple viewer for variant call format using htslib

Language: C++ - Size: 3.56 MB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 30 - Forks: 4

zhanxw/seqminer

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

Language: C - Size: 6.99 MB - Last synced: 4 days ago - Pushed: 3 months ago - Stars: 30 - Forks: 12

Rillke/Contact-Conversion-Wizard

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

Language: C# - Size: 709 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 28 - Forks: 10

ShixiangWang/Variants2Neoantigen

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

Language: Shell - Size: 546 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 27 - Forks: 8

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

Language: HTML - Size: 148 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 27 - Forks: 7

tjparnell/biotoolbox

Tools for querying and analysis of genomic data

Language: Perl - Size: 7.34 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 27 - Forks: 16

aquaskyline/16GT

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

Language: Perl - Size: 1.26 MB - Last synced: 2 days ago - Pushed: 5 months ago - Stars: 27 - Forks: 8

umccr/vcf_stuff

📊Evaluating, filtering, comparing, and visualising VCF

Language: Jupyter Notebook - Size: 40.3 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 26 - Forks: 3

jhbruhn/eurorack

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

Language: C++ - Size: 43.6 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 24 - Forks: 6

ncherric/Iliad

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Language: Python - Size: 54.7 MB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 23 - Forks: 2

fritzsedlazeck/SVCollector

Method to optimally select samples for validation and resequencing

Language: C++ - Size: 1.98 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 23 - Forks: 5

ShujiaHuang/cmdbtools

Command line tools for CMDB varaints browser

Language: Python - Size: 1.48 MB - Last synced: 5 days ago - Pushed: almost 2 years ago - Stars: 23 - Forks: 7

bolorundurowb/vCardLib

A .NET standard library for reading vCard files

Language: C# - Size: 805 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 22 - Forks: 14

wassermanlab/Variant_catalogue_pipeline

Variant catalogue pipeline

Language: HTML - Size: 5.78 MB - Last synced: 20 days ago - Pushed: 4 months ago - Stars: 22 - Forks: 7

vmware-samples/validated-solutions-for-cloud-foundation

A companion repository for the VMware Validated Solutions for VMware Cloud Foundation.

Language: Python - Size: 14.9 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 21 - Forks: 5

carjed/helmsman

highly-efficient & lightweight mutation signature matrix aggregation

Language: Python - Size: 14.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 19 - Forks: 5

Adron55/exceltovcf

Converting Excel(xlsx) to VCF(vCard)

Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 19 - Forks: 5

pimbongaerts/radseq

Collection of Python scripts for parsing/analyses of RAD-seq data

Language: Python - Size: 513 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 18 - Forks: 12

ngthomas/microhaplot

microhaplotype visualizer and analyzer

Language: Perl - Size: 19.8 MB - Last synced: 11 days ago - Pushed: almost 3 years ago - Stars: 18 - Forks: 5

OpenMendel/VCFTools.jl

Julia utilities for handling VCF files

Language: Julia - Size: 2.48 MB - Last synced: about 9 hours ago - Pushed: about 1 month ago - Stars: 18 - Forks: 4

clemgoub/TypeTE

Genotyping of segregating mobile elements insertions

Language: Perl - Size: 62.5 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 18 - Forks: 1

Zilong-Li/vcfpp

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

Language: C++ - Size: 1.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 18 - Forks: 3

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced: 28 days ago - Pushed: over 1 year ago - Stars: 18 - Forks: 12

shiquan/bcfanno

A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file

Language: C - Size: 214 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 17 - Forks: 5

citronalco/carddav2asterisk

Tiny Python script that reads all contacts from a CardDAV addressbook and inserts them into Asterisk's CID lookup database

Language: Python - Size: 32.2 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 17 - Forks: 4

ababaian/bioSyntax-archive 📦

Syntax highlighting for computational biology

Language: Vim script - Size: 22.5 MB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 16 - Forks: 2

BioInterchange/Ontologies

Home of the Genomic Feature and Variation Ontology (GFVO)

Language: Ruby - Size: 738 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 16 - Forks: 4

robertopreste/HmtNote 📦

Human mitochondrial variants annotation using HmtVar.

Language: Python - Size: 452 KB - Last synced: 24 days ago - Pushed: 7 months ago - Stars: 16 - Forks: 1

mpinese/nimpress

Polygenic score calculation from VCF in Nim.

Language: Nim - Size: 24.3 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 15 - Forks: 3

lifeomic/spark-vcf

Spark VCF data source implementation for Dataframes

Language: Scala - Size: 314 KB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 15 - Forks: 2

IPK-BIT/divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

Language: Svelte - Size: 2.6 MB - Last synced: 22 days ago - Pushed: 10 months ago - Stars: 15 - Forks: 1

sauternic/vCard-to-CSV

Makes vCard (.vcf) data readable

Language: HTML - Size: 444 KB - Last synced: 4 months ago - Pushed: over 5 years ago - Stars: 14 - Forks: 3

MRCIEU/gwas-vcf-specification

Specification for the GWAS-VCF format (manuscript in preparation)

Size: 11.8 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 14 - Forks: 1

danielecook/seq-collection

Language: Nim - Size: 6.83 MB - Last synced: 10 days ago - Pushed: over 3 years ago - Stars: 13 - Forks: 4

FolkerKinzel/VCards

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

Language: C# - Size: 85.9 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 13 - Forks: 4

HopedWall/rs-gfatovcf

Rust implementation of Flavia95's GFAtoVCF

Language: Rust - Size: 10.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 13 - Forks: 1

fritzsedlazeck/SURVIVOR_ant

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

Language: HTML - Size: 5.47 MB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 12 - Forks: 2

LBGC-CFB/SPiP

Splicing Prediction Pipeline

Language: R - Size: 39.4 MB - Last synced: 5 months ago - Pushed: 9 months ago - Stars: 12 - Forks: 4

cccnrc/plot-VCF

visual analysis of your VCF files

Language: R - Size: 75.9 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 12 - Forks: 2

py-vobject/vobject Fork of skarim/vobject

A full-featured Python package for parsing and creating iCalendar and vCard files

Language: Python - Size: 1.41 MB - Last synced: 7 days ago - Pushed: 20 days ago - Stars: 12 - Forks: 3

rasmushenningsson/VariantCallFormat.jl

Read and write VCF and BCF files

Language: Julia - Size: 917 KB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 12 - Forks: 3

varfish-org/mehari

VEP-like tool for sequence ontology and HGVS annotation of VCF files

Language: Rust - Size: 3.56 MB - Last synced: about 20 hours ago - Pushed: about 21 hours ago - Stars: 12 - Forks: 1

lindenb/hts-rdf

Managing sequencing data with RDF

Language: Makefile - Size: 90.8 KB - Last synced: 3 months ago - Pushed: 8 months ago - Stars: 11 - Forks: 0