variant-analysis

There are 3 repositories under variant-analysis topic.

HexraysToolbox
patois / HexraysToolbox
Hexrays Toolbox - Find code patterns within the Hexrays ctree
decompiler pattern-matching vulnerability-scanner ida-pro hex-rays hexrays hexrays-decompiler code-similarity bug-finding code-pattern-matching idapython-script idapython code-comparison reverse-engineering variant-analysis plagiarism-detection hexrays-toolbox loops ast ctree
Language:Python 474
biocommons / hgvs
Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).
bioinformatics genomics sequencing genome-analysis variant-analysis variation hgvs transcript
Language:Python 286
brentp / slivar
genetic variant expressions, annotation, and filtering for great good.
genomics rare-disease rare-variant-analysis variant-analysis variant-interpretation
Language:Nim 267
githubsatelliteworkshops / codeql
GitHub Satellite 2020 workshops on finding security vulnerabilities with CodeQL for Java/JavaScript.
2020 codeql satellite security variant-analysis workshops
211
brentp / echtvar
using all the bits for echt rapid variant annotation and filtering
genomics genetic-variants variant-annotations variant-analysis
Language:Rust 152
KarchinLab / open-cravat
A modular annotation tool for genomic variants
annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations
Language:JavaScript 137
yjx1217 / simuG
simuG: a general-purpose genome simulator
simulation genomics variant-analysis structural-variation
Language:Perl 96
Illumina / PlatinumGenomes
The Platinum Genomes Truthset
variant-analysis snvs indels
89
AppThreat / atom
atom is a novel intermediate representation for applications and a standalone tool that is powered by chen.
code-analysis supply-chain intermediate-representation application-analytics exploit-prediction reachability-analysis variant-analysis vulnerability-analysis
Language:Rust 73
RWilton / Arioc
Arioc: GPU-accelerated DNA short-read alignment
bioinformatics bisulfite-sequencing c-plusplus cuda dna-sequence-alignment genomics gpu methylation read-aligners sequence-alignment variant-analysis
70
KalinNonchev / gnomAD_DB
This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.
database genetics rare-variant-analysis gnomad annotation variant-analysis
Language:Python 50
biocommons / biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
bioinformatics genome-analysis genomics sequencing variant-analysis variation
Language:Python 47
bio-ontology-research-group / phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
translationalscience variant-analysis variant-annotations prioritize-disease-variants rare-variants phenotypes vcf-files omim synthetic-genomes variants disease
Language:Java 39
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 38
Illumina / witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
benchmarking cnv copy-number-variation structural-variation variant-analysis variants
Language:C# 33
biocommons / bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
bioinformatics genome-analysis genomics sequencing variant-analysis variation
Language:Python 23
Zilong-Li / vcfpp
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
bioinformatics htslib vcf genomics population-genetics variant-analysis
Language:C++ 23
mklarqvist / tachyon
High-level API for storing and querying sequence variant data
bioinformatics compression genetics genomics variant-analysis
Language:C++ 20
Yandell-Lab / VVP-pub
VVP (VAAST Variant Prioritizer) rapidly prioritizes genetic variants
variant-analysis
Language:C 19
bihealth / auto-acmg
Automatic classification of sequence variants and CNVs according to ACMG criteria.
algorithm variant-analysis acmg-guidelines
Language:Python 17
biocommons / anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
bioinformatics genome-analysis variant-analysis variation genomics sequencing
Language:Python 16
Illumina / happyR
R tools to interact with hap.py output
bioinformatics vcf-comparison variant-analysis r
Language:R 16
jonas-fuchs / virHEAT
Visualize microbial evolution at the SNP level!
genome-visualization heatmap pypi-package snps variant-analysis vcf-files viral-genomics
Language:Python 15
broadinstitute / g2papi
Python Client Library for the G2P Portal API
bioinformatics bioinformatics-tool bioinformatics-visualization isoforms protein-structure proteins sequence-alignment variant-analysis
Language:Python 13
nickzren / atav
A comprehensive platform for population-scale genomic analyses
population-genetics gene-discovery diagnostic-tool variant-analysis large-scale-genomics
Language:Java 12
Triti-Map
fei0810 / Triti-Map
A Snakemake-based pipeline for gene mapping in Triticeae.
bioinformatics epigenetics genomics snakemake variant-analysis
Language:Python 11
tatajuba
quadram-institute-bioscience / tatajuba
Identification and classification of homopolymeric tracts from reads.
bioinformatics genomics phylogenetics variant-analysis
Language:C 8
dbmi-bgm / granite
A collection of software to work with genomic variants
vcf variants variant-analysis trio de-novo-mutation compound-heterozygous de-novo-mutations variant-filtration snv snvs single-nucleotide-variation
Language:Python 7
elowy01 / vcf_filtering
Filter a VCF to discard false positive variants
machine-learning variant-calling variant-analysis genomics variant-filtration nextflow-pipelines
Language:Python 7
EUCANCan / variant-extractor
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
variant-analysis variant-calling vcf
Language:Python 7
Illumina / happyCompare
Reporting toolbox for happy output
bioinformatics r variant-analysis benchmarking
Language:R 7
ucdavis-bioinformatics-training / 2017-August-Variant-Analysis-Workshop
From SNP and structural variant calling to GWAS.
workshop-materials bioinformatics variant-analysis
Language:HTML 7
biocommons / seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
bioinformatics genome-analysis genomics sequencing variant-analysis variation
Language:Python 6
NCBI-Hackathons / Complex_Phenogeno
Mapping complex genotypes to phenotypic subclusters
variant-analysis visiting-bioinformatician phenotype
Language:Python 6
shiltemann / Virtual-Normal-Correction
Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full
genomics variant-analysis cancer-genomics
Language:Shell 6
tsnorri / vcf2multialign
Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.
bioinformatics variant-analysis haplotypes founder-sequences
Language:C++ 6