variant-analysis
There are 91 repositories under variant-analysis topic.
patois/HexraysToolbox
Hexrays Toolbox - Find code patterns within the Hexrays ctree
biocommons/hgvs
Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
githubsatelliteworkshops/codeql
GitHub Satellite 2020 workshops on finding security vulnerabilities with CodeQL for Java/JavaScript.
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
KarchinLab/open-cravat
A modular annotation tool for genomic variants
yjx1217/simuG
simuG: a general-purpose genome simulator
Illumina/PlatinumGenomes
The Platinum Genomes Truthset
AppThreat/atom
atom is a novel intermediate representation for applications and a standalone tool that is powered by chen.
RWilton/Arioc
Arioc: GPU-accelerated DNA short-read alignment
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.
biocommons/biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
bio-ontology-research-group/phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
cccnrc/plot-VCF
visual analysis of your VCF files
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
biocommons/bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
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.
mklarqvist/tachyon
High-level API for storing and querying sequence variant data
Yandell-Lab/VVP-pub
VVP (VAAST Variant Prioritizer) rapidly prioritizes genetic variants
bihealth/auto-acmg
Automatic classification of sequence variants and CNVs according to ACMG criteria.
biocommons/anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
Illumina/happyR
R tools to interact with hap.py output
jonas-fuchs/virHEAT
Visualize microbial evolution at the SNP level!
broadinstitute/g2papi
Python Client Library for the G2P Portal API
nickzren/atav
A comprehensive platform for population-scale genomic analyses
fei0810/Triti-Map
A Snakemake-based pipeline for gene mapping in Triticeae.
quadram-institute-bioscience/tatajuba
Identification and classification of homopolymeric tracts from reads.
dbmi-bgm/granite
A collection of software to work with genomic variants
elowy01/vcf_filtering
Filter a VCF to discard false positive variants
EUCANCan/variant-extractor
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
Illumina/happyCompare
Reporting toolbox for happy output
ucdavis-bioinformatics-training/2017-August-Variant-Analysis-Workshop
From SNP and structural variant calling to GWAS.
biocommons/seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
NCBI-Hackathons/Complex_Phenogeno
Mapping complex genotypes to phenotypic subclusters
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
tsnorri/vcf2multialign
Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.