vcf-files

There are 1 repository under vcf-files topic.

• edgardomortiz / vcf2phylip

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

  vcfsnpsphylipalignmentphylogeneticsnexusbinarysnappfastaoutgroupconvert-snpsvcf-filesphylogenetic-analysisvcf-formatphylip-matrixhaploiddiploidpolyploid
  Language:Python 307

• googlegenomics / gcp-variant-transforms

  GCP Variant Transforms

  vcf-filesbigquerydataflowbeam
  Language:Python 141

• zhanxw / rvtests

  Rare variant test software for next generation sequencing data

  next-generation-sequencingngsassociation-analysisgwasrare-variantmeta-analysisgenotypeskatc-plus-plusvariantsumichgeneticskernelvcf-files
  Language:C++ 140

• davetang / learning_vcf_file

  Learning the Variant Call Format

  vcfvcftoolsbcftoolsvcf-formatmulti-sample-vcfvcf-filescall-variantsgatk
  Language:Perl 139
• SNPGenie

  chasewnelson / SNPGenie

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

  snp-reportfasta-sequencesnext-generation-sequencingdnds-estimationdndsnucleotidediversity-measurementnucleotide-diversitysequence-analysispopulation-geneticsevolutionmolecular-evolutionevolutionary-parameterssubstitution-ratenei-gojoborinatural-selectionvcfvcf-filesperl
  Language:Perl 111

• Al-Murphy / MungeSumstats

  Rapid standardisation and quality control of GWAS or QTL summary statistics

  bioinformaticsrgwassummary-statisticsbioconductor-packager-packagestandardisationgenomicsvcf-filesdatabase-apiqtl
  Language:R 79

• pwwang / vcfstats

  Powerful statistics for VCF files

  vcfvcf-filesvcfstats
  Language:Python 69

• jonas-fuchs / BAMdash

  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

  bam-filesbed-filescoverage-reportdashboardgenbank-filesinteractiveplotlyvcf-files
  Language:Python 54

• everestial / VCF-Simplify

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

  vcfpython-parservariant-annotationhaplotypesphasingconvertsphase-stitcherphase-extendertableviewvcf-filesvcftoolschrom
  Language:Python 49

• bio-ontology-research-group / phenomenet-vp

  A phenotype-based tool for variant prioritization in WES and WGS data

  translationalsciencevariant-analysisvariant-annotationsprioritize-disease-variantsrare-variantsphenotypesvcf-filesomimsynthetic-genomesvariantsdisease
  Language:Java 38

• cccnrc / plot-VCF

  visual analysis of your VCF files

  geneticsgenomegenome-analysisgenome-graphgraphgraphicsgraphics-programmingplotplot-generatorvariant-analysisvariant-annotationsvariantsvcfvcf-filesvisual-analysisvisualization
  Language:R 36

• py-vobject / vobject

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

  caldavcarddavicalendarvcalendarvcardvcard-parsericsvcfvcf-files
  Language:Python 34

• dancooke / starfish

  Intersect multiple VCF files with haplotype awareness

  vcf-fileshaplotypesintersectioncompare-filesvariant-calls
  Language:Python 25

• ikmb / vcf2prot

  Accelerate the generation of personalized proteomes from a Variant calling format (VCF) file and a reference proteome using graphical processing units (GPUs).

  geneticsprotein-sequencesvcf-filesvcf-converterrust-langproteomicsrust-library
  Language:Rust 17
• SMS-backup-and-restore-extractor

  raleighlittles / SMS-backup-and-restore-extractor

  A simple Python script for extracting images out of an "SMS Backup & Restore" backup.

  sms-backup-and-restoreriteshsahulxml-xpathbase64vcardvcard-parservcf-files
  Language:Python 17

• jonas-fuchs / virHEAT

  Visualize microbial evolution at the SNP level!

  genome-visualizationheatmappypi-packagesnpsvariant-analysisvcf-filesviral-genomics
  Language:Python 15

• lifeomic / spark-vcf

  Spark VCF data source implementation for Dataframes

  dataframegenomicsgenotypelifeomicsparkspark-sqlteam-clinical-intelligencevariantsvcfvcf-files
  Language:Scala 14

• rasmushenningsson / VariantCallFormat.jl

  Read and write VCF and BCF files

  vcfbcfvcf-filesbioinformaticsjuliagenetics
  Language:Julia 13

• biodata-fun / htslib_howto

  Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts

  htslibcsamvcf-filescram-filessam-filesbam-filesgenomic-data-analysisfastq-files
  Language:C 11

• chasewnelson / EBT

  Evolutionary Bioinformatics Toolkit (EBT)

  perlvcfvcf-filesfastafasta-sequencessequencesequence-alignmentgtfgffdna-sequences
  Language:Perl 11

• isinaltinkaya / vcfgl

  Genotype likelihood simulator for VCF/BCF files

  genotype-likelihoodsmsprimesimulationtskitvcfvcf-files
  Language:C++ 10

• mobidic / MobiCNV

  CNV analysis based on the depth of coverage of Illumina data

  bioinformatics-toolgene-panelscoverage-filesvcf-filestsv-filescnv-analysis
  Language:Python 8

• USDA-VS / vSNP3

  vSNP -- validate SNPs

  bam-filessnpsanalysis-pipelinebrucellafreebayesgenomicshigh-throughput-sequencinginfluenzamycobacterium-tuberculosis-complexphylogeneticspipelinesars-cov-2tuberculosisvcf-fileswgswhole-genome-sequencingmycobacterium-bovismycobacterium-bovis-af2122bwa-mem
  Language:Python 8
• fritzbox_phonebook_convert_xml_csv_vcf

  soerenj / fritzbox_phonebook_convert_xml_csv_vcf

  Converts phonebook Fritzbox between .xml <=> .csv or .vcf (webapp) ; DE: konvertiert Telefonbuch Datei

  fritzboxfritzbox-adressbuchjavascriptvcfvcardphonebookcsvvcf-filesxmlfritzbox-xmlconverts-phonebook-fritzbox
  Language:HTML 7

• cartoonist / vcfy

  VCF file synthesiser with random variants

  vcfvcf-filesvariant-simulation
  Language:Python 6

• bolorundurowb / VCF-Reader

  vcf file reader

  gtk-sharpcsharpvcardvcfvcf-files
  Language:C# 5

• Aptivi / VisualCard

  A .NET vCard parser with Android contacts2.db and MeCard support

  contactcontactscsharpcsharp-librarydotnetdotnet-coredotnet-frameworklibraryvcfcontact-managementcontact-management-systemcontact-managercontact-manager-apicsharp-codecsharp-liblibrariesvcf-datavcf-filesvcftoolsvcf-5
  Language:C# 4

• Tohidkhan6332 / Contact

  Simple VCF

  connectvcf-files
  Language:HTML 4

• ALAPY / AGx

  Variant annotation and filtration server ALAPY Genome Explorer

  ngsvcf-filesvcftoolsvcf-datavariant-annotationsvariant-analysisvcf
  Language:Shell 3

• antonio-nicolau / vcard-formatter

  Dart library to read and write vCard files.

  dartvcardvcf-files
  Language:Dart 3

• iqbal-lab-org / ivcfmerge

  A utility to merge a large number of VCF files incrementally

  variant-call-formatvcfvcf-filesvcfs
  Language:Python 3

• Juni4567 / VCF-to-CSV

  This Utility software converts VCF files into CSV format as an Excel sheet.

  csvdownloadexcel-sheetexenodevcf-files
  Language:JavaScript 3

• kcleal / zights

  htslib for the zig build system

  bam-filescram-filesgenomicshtslibvcf-files
  Language:Zig 3

• matt-sd-watson / pymongo-vcf

  Integration of a MongoDB database for storing and filtering variant caller (VCF) file information

  mongodbvcf-filesdatabasenosql-databasevcfpymongo-vcf
  Language:Jupyter Notebook 3
• HaploDynamics

  remytuyeras / HaploDynamics

  A python library to develop genomic data simulators

  allele-frequenciesgenomics-datahardy-weinberg-equilibriumlinkage-disequilibriumpopulation-geneticspopulation-genomicssimulationsimulatorvcfvcf-filesgwasgwas-datasetdnadna-sequencesgenomicsmicroarray-data
  Language:Python 3

• sennpuuki / convert-Plink-to-VCF-format

  plinkvcfvcf-filesplink-filesformat-converter
  Language:Python 3