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
vcf snps phylip alignment phylogenetics nexus binary snapp fasta outgroup convert-snps vcf-files phylogenetic-analysis vcf-format phylip-matrix haploid diploid polyploid
Language:Python 270
davetang / learning_vcf_file
Learning the Variant Call Format
vcf vcftools bcftools vcf-format multi-sample-vcf vcf-files call-variants gatk
Language:Perl 136
googlegenomics / gcp-variant-transforms
GCP Variant Transforms
beam bigquery dataflow vcf-files
Language:Python 134
zhanxw / rvtests
Rare variant test software for next generation sequencing data
association-analysis c-plus-plus genetics genotype gwas kernel meta-analysis next-generation-sequencing ngs rare-variant skat umich variants vcf-files
Language:C++ 126
SNPGenie
chasewnelson / SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
diversity-measurement dnds dnds-estimation evolution evolutionary-parameters fasta-sequences molecular-evolution natural-selection nei-gojobori next-generation-sequencing nucleotide nucleotide-diversity perl population-genetics sequence-analysis snp-report substitution-rate vcf vcf-files
Language:Perl 100
neurogenomics / MungeSumstats
Rapid standardisation and quality control of GWAS or QTL summary statistics
bioinformatics r gwas summary-statistics bioconductor-package r-package standardisation genomics vcf-files database-api qtl
Language:R 69
pwwang / vcfstats
Powerful statistics for VCF files
vcf vcf-files vcfstats
Language:Python 58
everestial / VCF-Simplify
A python parser to simplify and build the VCF (Variant Call Format).
chrom converts haplotypes phase-extender phase-stitcher phasing python-parser tableview variant-annotation vcf vcf-files vcftools
Language:Python 45
bio-ontology-research-group / phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
disease omim phenotypes prioritize-disease-variants rare-variants synthetic-genomes translationalscience variant-analysis variant-annotations variants vcf-files
Language:Java 35
cccnrc / plot-VCF
visual analysis of your VCF files
genetics genome genome-analysis genome-graph graph graphics graphics-programming plot plot-generator variant-analysis variant-annotations variants vcf vcf-files visual-analysis visualization
Language:R 24
dancooke / starfish
Intersect multiple VCF files with haplotype awareness
vcf-files haplotypes intersection compare-files variant-calls
Language:Python 22
jonas-fuchs / BAMdash
create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
bam-files bed-files coverage-report dashboard genbank-files interactive plotly vcf-files
Language:Python 21
py-vobject / vobject
A full-featured Python package for parsing and creating iCalendar and vCard files
caldav carddav icalendar vcalendar vcard vcard-parser ics vcf vcf-files
Language:Python 18
lifeomic / spark-vcf
Spark VCF data source implementation for Dataframes
dataframe genomics genotype lifeomic spark spark-sql team-clinical-intelligence variants vcf vcf-files
Language:Scala 14
ikmb / vcf2prot
Accelerate the generation of personalized proteomes from a Variant calling format (VCF) file and a reference proteome using graphical processing units (GPUs).
genetics protein-sequences vcf-files vcf-converter rust-lang proteomics rust-library
Language:Rust 13
rasmushenningsson / VariantCallFormat.jl
Read and write VCF and BCF files
vcf bcf vcf-files bioinformatics julia genetics
Language:Julia 12
chasewnelson / EBT
Evolutionary Bioinformatics Toolkit (EBT)
perl vcf vcf-files fasta fasta-sequences sequence sequence-alignment gtf gff dna-sequences
Language:Perl 11
CATE
theLongLab / CATE
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
1000genomes cuda cuda-programming cuda-toolkit ehh evolutionary-algorithms evolutionary-biology evolutionary-computation extended-haplotype-homozygosity genetic-algorithm genetics mk-test neutrality neutrality-test tajima vcf vcf-data vcf-files
Language:Cuda 11
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
htslib c sam vcf-files cram-files sam-files bam-files genomic-data-analysis fastq-files
Language:C 10
jonas-fuchs / virHEAT
Visualize microbial evolution at the SNP level!
genome-visualization heatmap pypi-package snps variant-analysis vcf-files viral-genomics
Language:Python 10
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-restore riteshsahu lxml-xpath base64 vcard vcard-parser vcf-files
Language:Python 10
mobidic / MobiCNV
CNV analysis based on the depth of coverage of Illumina data
bioinformatics-tool gene-panels coverage-files vcf-files tsv-files cnv-analysis
Language:Python 8
isinaltinkaya / vcfgl
Genotype likelihood simulator for VCF/BCF files
genotype-likelihoods msprime simulation tskit vcf vcf-files
Language:C++ 7
cartoonist / vcfy
VCF file synthesiser with random variants
vcf vcf-files variant-simulation
Language:Python 6
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
fritzbox fritzbox-adressbuch javascript vcf vcard phonebook csv vcf-files xml fritzbox-xml converts-phonebook-fritzbox
Language:HTML 6
bolorundurowb / VCF-Reader
vcf file reader
gtk-sharp csharp vcard vcf vcf-files
Language:C# 5
USDA-VS / vSNP3
vSNP -- validate SNPs
bam-files snps analysis-pipeline brucella freebayes genomics high-throughput-sequencing influenza mycobacterium-tuberculosis-complex phylogenetics pipeline sars-cov-2 tuberculosis vcf-files wgs whole-genome-sequencing mycobacterium-bovis mycobacterium-bovis-af2122 bwa-mem
Language:Python 4
ALAPY / AGx
Variant annotation and filtration server ALAPY Genome Explorer
ngs vcf-files vcftools vcf-data variant-annotations variant-analysis vcf
Language:Shell 3
iqbal-lab-org / ivcfmerge
A utility to merge a large number of VCF files incrementally
vcf-files variant-call-format vcf vcfs
Language:Python 3
Juni4567 / VCF-to-CSV
This Utility software converts VCF files into CSV format as an Excel sheet.
node vcf-files csv excel-sheet exe download
Language:JavaScript 3
sennpuuki / convert-Plink-to-VCF-format
plink vcf vcf-files plink-files format-converter
Language:Python 3
antonio-nicolau / vcard-formatter
Dart library to read and write vCard files.
dart vcard vcf-files
Language:Dart 2
Aptivi / VisualCard
A .NET vCard parser with Android contacts2.db and MeCard support
contact contacts csharp csharp-library dotnet dotnet-core dotnet-framework library vcf contact-management contact-management-system contact-manager contact-manager-api csharp-code csharp-lib libraries vcf-data vcf-files vcftools vcf-5
Language:C# 2
SNPio
btmartin721 / SNPio
API to read, write, and filter DNA sequence alignment files
dna-sequence-alignment file-converter filtering genotypes input-output minor-allele-frequency missing-data phylip plots principal-component-analysis snps structure-alignment vcf-files
Language:Python 2
cntct-app / cntct
group contact card sharing made easy ✨
contact-sharing contacts vcard vcf-files react styled-components
Language:JavaScript 2
HaploDynamics
remytuyeras / HaploDynamics
A python library to develop genomic data simulators
allele-frequencies genomics-data hardy-weinberg-equilibrium linkage-disequilibrium population-genetics population-genomics simulation simulator vcf vcf-files gwas gwas-dataset dna dna-sequences genomics microarray-data
Language:Python 2