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Search results for variants vcf
variants
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vcf
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17 search results found
Vg
⭐
1,022
tools for working with genome variation graphs
Samplot
⭐
458
Plot structural variant signals from many BAMs and CRAMs
Snippy
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408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
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
Igv Reports
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298
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
Hap.py
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283
Haplotype VCF comparison tools
Rtg Tools
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260
RTG Tools: Utilities for accurate VCF comparison and manipulation
Pcgr
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234
Personal Cancer Genome Reporter (PCGR)
Vcfr
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225
Tools to work with variant call format files
Slivar
⭐
221
genetic variant expressions, annotation, and filtering for great good.
Svaba
⭐
211
Structural variation and indel detection by local assembly
Smoove
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173
structural variant calling and genotyping with existing tools, but, smoothly.
Nirvana
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158
The nimble & robust variant annotator
Lancet
⭐
145
Microassembly based somatic variant caller for NGS data
Hgvs
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142
HGVS variant name parsing and generation
Poplddecay
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138
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Mutscan
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127
Detect and visualize target mutations by scanning FastQ files directly
Gqt
⭐
125
A genotype query interface.
Learning_vcf_file
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122
Learning the Variant Call Format
Variantspark
⭐
121
machine learning for genomic variants
Gcp Variant Transforms
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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.
Vcf Kit
⭐
107
VCF-kit: Assorted utilities for the variant call format
Genomewarp
⭐
96
GenomeWarp translates genetic variants from one genome assembly version to another.
Expecto
⭐
95
predicting expression effects of human genome variants ab initio from sequence
Gatk4 Germline Snps Indels
⭐
88
Workflows for germline short variant discovery with GATK4
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
Parliament2
⭐
83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtyper
⭐
78
Bayesian genotyper for structural variants
Duphold
⭐
73
don't get DUP'ed or DEL'ed by your putative SVs.
Variantvisualization.jl
⭐
72
Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
Mocha
⭐
70
MOsaic CHromosomal Alterations (MoChA) caller
Bcbio.variation
⭐
66
Toolkit to analyze genomic variation data, built on the GATK with Clojure
Vcfgo
⭐
55
a golang library to read, write and manipulate files in the variant call format.
Tiddit
⭐
55
TIDDIT - structural variant calling
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.
Spvcf
⭐
54
Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently
Vawk
⭐
53
An awk-like VCF parser
Jannovar
⭐
51
Annotation of VCF variants with functional impact and from databases (executable+library)
Cpsr
⭐
50
Cancer Predisposition Sequencing Reporter (CPSR)
Vembrane
⭐
50
vembrane filters VCF records using python expressions
Vcfstats
⭐
48
Powerful statistics for VCF files
Sv Plaudit
⭐
47
Pipeline for structural variant image curation and analysis.
Svviz2
⭐
46
for visual evaluation of read support for structural variation
Smash
⭐
43
Benchmarking toolkit for variant calling
Gvanno
⭐
43
Generic human DNA variant annotation pipeline
Platinumgenomes
⭐
42
The Platinum Genomes Truthset
Hts Nim Tools
⭐
41
useful command-line tools written to show-case hts-nim
Analysis_pipeline
⭐
40
TOPMed analysis pipeline
Broad Prod Wgs Germline Snps Indels
⭐
39
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-geno
Gtctovcf
⭐
39
Script to convert GTC/BPM files to VCF
Dipcall
⭐
38
Reference-based variant calling pipeline for a pair of phased haplotype assemblies
Glia
⭐
34
a string to graph aligner
Cycledash
⭐
34
Variant Caller Analysis Dashboard and Data Management System
Vcf_parser
⭐
32
Simple vcf parser, based on PyVCF
Introgression Detection
⭐
31
Browsevcf
⭐
29
BrowseVCF is a web-based application and workflow to quickly prioritise disease-causative variants in VCF files.
Mutserve
⭐
29
mtDNA Variant Caller
Seqminer
⭐
28
Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
Sviper
⭐
28
Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
Isown
⭐
28
Thesis
⭐
28
my PhD thesis
Phenix
⭐
27
Public Health England SNP calling pipeline.
Hapdip
⭐
27
The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data
Flopp
⭐
27
flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.
Witty.er
⭐
26
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Svdb
⭐
26
structural variant database software
Cnv_facets
⭐
26
Somatic copy variant caller (CNV) for next generation sequencing
Cerebra
⭐
26
A tool for fast and accurate summarizing of variant calling format (VCF) files
Vcf
⭐
26
Variant Call Format parser library for Go
Graphite
⭐
25
Graphite - Graph-based variant adjudication
Variant Filter
⭐
25
A false-positive filter for variants called from massively parallel sequencing
Pandasvcf
⭐
25
VCF parser using the Python pandas library
Svv
⭐
24
Stupid Simple Structural Variant View
Gvcfgenotyper
⭐
23
A utility for merging and genotyping Illumina-style GVCFs.
Vapr
⭐
23
VAPr: A Python package for NoSQL variant data storage, annotation and prioritization
1000_genomes_examples
⭐
23
Examples using R and 1000 genomes data
Unfazed
⭐
23
Unfazed by genomic variant phasing
Svpv
⭐
23
Structural Variant Prediction Viewer
Cutevcf
⭐
23
simple viewer for variant call format using htslib
Vcf.js
⭐
22
A VCF parser and variant record model in JavaScript.
Samovar
⭐
22
Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
Tapes
⭐
21
TAPES : a Tool for Assessment and Prioritisation in Exome Studies
Cmdbtools
⭐
21
Command line tools for CMDB varaints browser
Hapcut
⭐
21
program for haplotype phasing from sequence reads and related tools
Forestqc
⭐
21
Quality control on genetic variants from next-generation sequencing data using random forest
Pathoscore
⭐
21
pathoscore evaluates variant pathogenicity tools and scores.
Checkvcf
⭐
20
Sanity check Variant Call Format (VCF) files.
Varianttoolchest
⭐
20
VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful tools: (1) SetOperator for performing powerful set operations; and (2) VarStats for various statistics on VCF files.
Vcf2fhir
⭐
20
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Vcf_stuff
⭐
19
📊Evaluating, filtering, comparing, and visualising VCF
Automap
⭐
19
Tool to find regions of homozygosity (ROHs) from sequencing data.
Rtgeval
⭐
19
Wrapper for RTG's vcfeval; DEPRECATED!
Crisp
⭐
19
Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
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