spark-vcfSpark VCF data source implementation for Dataframes
Stars: ✭ 15 (-53.12%)
SNPGenieProgram for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Stars: ✭ 81 (+153.13%)
2vcfconvert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations
Stars: ✭ 42 (+31.25%)
calcardbackupcalcardbackup: moved to https://codeberg.org/BernieO/calcardbackup
Stars: ✭ 67 (+109.38%)
phenomenet-vpA phenotype-based tool for variant prioritization in WES and WGS data
Stars: ✭ 31 (-3.12%)
vcf stuff📊Evaluating, filtering, comparing, and visualising VCF
Stars: ✭ 19 (-40.62%)
CuteVCFsimple viewer for variant call format using htslib
Stars: ✭ 30 (-6.25%)
laravel-vcardA fluent builder class for vCard files.
Stars: ✭ 29 (-9.37%)
rvtestsRare variant test software for next generation sequencing data
Stars: ✭ 114 (+256.25%)
vembranevembrane filters VCF records using python expressions
Stars: ✭ 46 (+43.75%)
Variants2NeoantigenA neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
Stars: ✭ 27 (-15.62%)
csv2vcf🔧 Simple script in python to convert CSV files to VCF
Stars: ✭ 66 (+106.25%)
cljamA DNA Sequence Alignment/Map (SAM) library for Clojure
Stars: ✭ 85 (+165.63%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+678.13%)
Snippy✂️ ⚡️ Rapid haploid variant calling and core genome alignment
Stars: ✭ 245 (+665.63%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+659.38%)
Vcf2mafConvert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Stars: ✭ 229 (+615.63%)
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+587.5%)
SurvivorToolset for SV simulation, comparison and filtering
Stars: ✭ 180 (+462.5%)
PcgrPersonal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (+425%)
BiosyntaxSyntax highlighting for computational biology
Stars: ✭ 164 (+412.5%)
Vcf2phylipConvert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Stars: ✭ 126 (+293.75%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (+215.63%)
ParagraphGraph realignment tools for structural variants
Stars: ✭ 92 (+187.5%)
TruvariStructural variant toolkit for VCFs
Stars: ✭ 85 (+165.63%)
SvtyperBayesian genotyper for structural variants
Stars: ✭ 79 (+146.88%)
GenozipCompressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too
Stars: ✭ 53 (+65.63%)
16gtSimultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Stars: ✭ 26 (-18.75%)
Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-18.75%)
GvannoGeneric germline variant annotation pipeline
Stars: ✭ 23 (-28.12%)
Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-40.62%)
HailScalable genomic data analysis.
Stars: ✭ 706 (+2106.25%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+1553.13%)
VcardThis vCard PHP library can easily parse or generate/export vCards as .vcf
Stars: ✭ 333 (+940.63%)
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+715.63%)
Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
Stars: ✭ 259 (+709.38%)
VCF-kitVCF-kit: Assorted utilities for the variant call format
Stars: ✭ 94 (+193.75%)
23andme2vcfconvert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
Stars: ✭ 91 (+184.38%)
OntologiesHome of the Genomic Feature and Variation Ontology (GFVO)
Stars: ✭ 16 (-50%)
TypeTEGenotyping of segregating mobile elements insertions
Stars: ✭ 15 (-53.12%)
vcf2gwasPython API for comprehensive GWAS analysis using GEMMA
Stars: ✭ 27 (-15.62%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (-37.5%)
jannovarAnnotation of VCF variants with functional impact and from databases (executable+library)
Stars: ✭ 42 (+31.25%)
cutevariantA standalone and free application to explore genetics variations from VCF file
Stars: ✭ 61 (+90.63%)
vcf2tsvGenomic VCF to tab-separated values
Stars: ✭ 27 (-15.62%)
fucFrequently used commands in bioinformatics
Stars: ✭ 23 (-28.12%)
ilusA handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
Stars: ✭ 64 (+100%)
cpsrCancer Predisposition Sequencing Reporter (CPSR)
Stars: ✭ 44 (+37.5%)
indelopefind large indels (in the blind spot between GATK/freebayes and SV callers)
Stars: ✭ 38 (+18.75%)
snpstools for reading, writing, merging, and remapping SNPs
Stars: ✭ 57 (+78.13%)
starfishIntersect multiple VCF files with haplotype awareness
Stars: ✭ 19 (-40.62%)