vcf

There are 11 repositories under vcf topic.

hail
hail-is / hail
Cloud-native genomic dataframes and batch computing
genetics vcf genomics gwas bioinformatics python software hail
Language:Python 951
samtools / htslib
C library for high-throughput sequencing data formats
bam bcf bioinformatics cram htslib ngs sam vcf
Language:C 784
jeroendesloovere / vcard
This vCard PHP library can easily parse or generate/export vCards as .vcf
vcard vcard-php vcf php
Language:PHP 495
tseemann / snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
variant-calling haploid bacteria fastq-analysis snps vcf indel-discovery bioinformatics genomics
Language:Perl 446
Illumina / hap.py
Haplotype VCF comparison tools
bioinformatics genomics vcf vcf-comparison
Language:C++ 399
mskcc / vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
isoforms maf perl vcf vep
Language:Perl 363
brentp / cyvcf2
cython + htslib == fast VCF and BCF processing
bioinformatics cython genomics htslib vcf
Language:Cython 362
brentp / vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
annotation bioinformatics genomics vcf
Language:Go 353
fritzsedlazeck / SURVIVOR
Toolset for SV simulation, comparison and filtering
bioinformatics structural-variations simulator comparison survivor vcf bioconda
Language:C++ 335
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf
Language:Python 308
truvari
ACEnglish / truvari
Structural variant toolkit for VCFs
annotation-tool benchmarking bioinformatics data-science genomics sequencing structural-variation sv-merging vcf vcf-comparison
Language:Python 299
samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
genomics sequencing dna ngs bam cram sam fasta vcf java-api java
Language:Java 275
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 271
bioSyntax / bioSyntax
Syntax highlighting for computational biology
bioinformatics computational-biology syntax-highlighting less vim gedit sublime-text bam vcf fasta pdb
Language:Shell 252
sigven / pcgr
Personal Cancer Genome Reporter (PCGR)
cancer-genomics cancer-variants somatic interpreter reporting-engine clinical oncology-data precision-oncology vcf tumor annotation-framework annotation-tool cancer copy-number-variation snvs therapeutic-targets precision-cancer-medicine variant-interpretation
Language:R 247
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 192
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
genomics compression fastq vcf bam sam fasta gvf 23andme gzip bgzip samtools bwa cram
Language:C 151
Illumina / paragraph
Graph realignment tools for structural variants
vcf htslib structural-variation variant-calling genotyping
Language:C++ 147
kcleal / gw
Genome browser and variant annotation
annotation-tool vcf bam-files cram-files genome-browser
Language:C++ 146
VariantSpark
aehrc / VariantSpark
machine learning for genomic variants
variant-spark gwas random-forest genome association-studies vcf variantspark notebook databricks bioinformatics aws emr
Language:JavaScript 138
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
brentp / peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
genomics vcf bioinformatics pedigree genotype ancestry
Language:Jupyter Notebook 129
hall-lab / svtyper
Bayesian genotyper for structural variants
bioinformatics genomics genotype vcf
Language:Python 123
AndersenLab / VCF-kit
VCF-kit: Assorted utilities for the variant call format
python vcf
Language:Python 121
jhermsmeier / node-vcf
A not so forgiving vCard / vcf parser
format jcard parser vcard vcf
Language:JavaScript 104
labsquare / cutevariant
A standalone and free application to explore genetics variations from VCF file
genetics variant-call-format vcf gui pyside2 python3
Language:Python 102
SNPGenie
chasewnelson / SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
snp-report fasta-sequences next-generation-sequencing dnds-estimation dnds nucleotide diversity-measurement nucleotide-diversity sequence-analysis population-genetics evolution molecular-evolution evolutionary-parameters substitution-rate nei-gojobori natural-selection vcf vcf-files perl
Language:Perl 100
arrogantrobot / 23andme2vcf
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
vcf 23andme ancestry annotations perl
Language:Perl 94
apriha / snps
tools for reading, writing, merging, and remapping SNPs
snps dna chromosomes bioinformatics vcf
Language:Python 91
chrovis / cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
clojure bioinformatics genomics sam bam vcf bcf fasta 2bit bed fastq wig bigwig gff cram
Language:Clojure 90
bihealth / vcfpy
Python 3 library with good support for both reading and writing VCF
bioinformatics vcf parsing writing file-format
Language:Python 89
TileDB-Inc / TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
genomics vcf variant-calling tiledb bioinformatics data-science spark python gwas
Language:C++ 82
frankvogt / vcf2gwas
Python API for comprehensive GWAS analysis using GEMMA
gwas vcf gemma-analysis
Language:Python 81
starskyzheng / panpop
Application of pan-genome for population
bioinformatics clustering genomics population-genetics structural-variations vcf panpop
Language:Perl 77
mixerp / MixERP.Net.VCards
vCard Serializer and Parser for C#
vcard vcf csharp dotnet
Language:C# 70
Moduland / csv2vcf
🔧 Simple script in python to convert CSV files to VCF
vcf csv converter python python3 comma-separated-values variant-calls tools script moduland contacts phone-number email-template phonebook phonebooks contact contacts-app contacts-manager contacts-book vcard
Language:Python 70