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Search results for vcf
vcf
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607 search results found
Picard
⭐
914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Htslib
⭐
762
C library for high-throughput sequencing data formats
Nucleus
⭐
675
Python and C++ code for reading and writing genomics data.
Bioawk
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518
BWK awk modified for biological data
Nanopolish
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496
Signal-level algorithms for MinION data
Vcard
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463
This vCard PHP library can easily parse or generate/export vCards as .vcf
Samplot
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458
Plot structural variant signals from many BAMs and CRAMs
Vcftools
⭐
415
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Cyvcf2
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345
cython + htslib == fast VCF and BCF processing
Vcfanno
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334
annotate a VCF with other VCFs/BEDs/tabixed files
Vcf2maf
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305
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Survivor
⭐
299
Toolset for SV simulation, comparison and filtering
Igv Reports
⭐
298
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
Truvari
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284
Structural variant toolkit for VCFs
Hap.py
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283
Haplotype VCF comparison tools
Genomics_general
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279
General tools for genomic analyses.
Htsjdk
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271
A Java API for high-throughput sequencing data (HTS) formats.
Rtg Tools
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260
RTG Tools: Utilities for accurate VCF comparison and manipulation
Pygeno
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242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Pcgr
⭐
234
Personal Cancer Genome Reporter (PCGR)
Vcfr
⭐
225
Tools to work with variant call format files
Somalier
⭐
224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Kipoi
⭐
222
Kipoi's model zoo API
Slivar
⭐
221
genetic variant expressions, annotation, and filtering for great good.
Vcf2phylip
⭐
216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Gridss
⭐
212
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Svaba
⭐
211
Structural variation and indel detection by local assembly
Somaticseq
⭐
185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Biosyntax
⭐
184
Syntax highlighting for computational biology
Smoove
⭐
173
structural variant calling and genotyping with existing tools, but, smoothly.
Nirvana
⭐
158
The nimble & robust variant annotator
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Rust Bio Tools
⭐
154
A set of command line utilities based on Rust-Bio.
Lancet
⭐
145
Microassembly based somatic variant caller for NGS data
Genozip
⭐
144
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
Hgvs
⭐
142
HGVS variant name parsing and generation
Paragraph
⭐
140
Graph realignment tools for structural variants
Poplddecay
⭐
138
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Vpim
⭐
133
vCard and iCalendar support for ruby
Sigprofilerextractor
⭐
132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Smcpp
⭐
131
SMC++ infers population history from whole-genome sequence data.
Mutscan
⭐
127
Detect and visualize target mutations by scanning FastQ files directly
Gqt
⭐
125
A genotype query interface.
Vcf Validator
⭐
125
Validation suite for Variant Call Format (VCF) files, implemented using C++11
Dsuite
⭐
123
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
Learning_vcf_file
⭐
122
Learning the Variant Call Format
Variantspark
⭐
121
machine learning for genomic variants
Gtc2vcf
⭐
119
Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
Gw
⭐
118
Genome browser and variant annotation
Jigv
⭐
115
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
Gcp Variant Transforms
⭐
114
GCP Variant Transforms
Clinvar
⭐
108
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
Easysfs
⭐
108
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Vcf Kit
⭐
107
VCF-kit: Assorted utilities for the variant call format
Ngscheckmate
⭐
106
Software program for checking sample matching for NGS data
Peddy
⭐
104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Ldblockshow
⭐
102
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
Pandora
⭐
98
Pan-genome inference and genotyping with long noisy or short accurate reads
Yhaplo
⭐
98
Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
Genomewarp
⭐
96
GenomeWarp translates genetic variants from one genome assembly version to another.
Node Vcf
⭐
95
A not so forgiving vCard / vcf parser
Expecto
⭐
95
predicting expression effects of human genome variants ab initio from sequence
Snpgenie
⭐
94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Neopredpipe
⭐
93
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
H3agwas
⭐
89
GWAS Pipeline for H3Africa
Gatk4 Germline Snps Indels
⭐
88
Workflows for germline short variant discovery with GATK4
Cljam
⭐
87
A DNA Sequence Alignment/Map (SAM) library for Clojure
Pipeline Structural Variation
⭐
87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Svim
⭐
85
Structural Variant Identification Method using Long Reads
Cutevariant
⭐
85
A standalone and free application to explore genetics variations from VCF file
Digital Business Card
⭐
84
An effort to evolve the old paper business card into newer social formats as Passbook, HTML5+hCard, VCF
Parliament2
⭐
83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
23andme2vcf
⭐
82
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
Snps
⭐
82
tools for reading, writing, merging, and remapping SNPs
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Vcfpy
⭐
78
Python 3 library with good support for both reading and writing VCF
Svtyper
⭐
78
Bayesian genotyper for structural variants
Bgt
⭐
76
Flexible genotype query among 30,000+ samples whole-genome
Duphold
⭐
73
don't get DUP'ed or DEL'ed by your putative SVs.
Neat Genreads
⭐
72
NEAT read simulation tools
Variantvisualization.jl
⭐
72
Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
Scoary
⭐
71
Pan-genome wide association studies
Mocha
⭐
70
MOsaic CHromosomal Alterations (MoChA) caller
Bio Vcf
⭐
69
Smart VCF parser DSL
Vcardeditor
⭐
68
Simple vCard (*.vcf) file Editor.
Genotype_plot
⭐
68
A set of functions to visualise genotypes based on a VCF
Hadoop Bam
⭐
66
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
Bcbio.variation
⭐
66
Toolkit to analyze genomic variation data, built on the GATK with Clojure
Haplogrep Cmd
⭐
64
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
Vcf2gwas
⭐
62
Python API for comprehensive GWAS analysis using GEMMA
Opengene.jl
⭐
61
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Local_pca
⭐
59
Methods for examining PCA locally along the genome.
Pyvcf
⭐
58
A Variant Call Format reader for Python.
Simug
⭐
58
simuG: a general-purpose genome simulator
Tiddit
⭐
55
TIDDIT - structural variant calling
Vcfgo
⭐
55
a golang library to read, write and manipulate files in the variant call format.
Transanno
⭐
54
accurate LiftOver tool for new genome assemblies
Gatk4 Somatic Snvs Indels
⭐
54
This repo will be archived soon, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
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