There are 3 repositories under variant-analysis topic.
Hexrays Toolbox - Find code patterns within the Hexrays ctree
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
GitHub Satellite 2020 workshops on finding security vulnerabilities with CodeQL for Java/JavaScript.
A modular annotation tool for genomic variants
non-redundant, compressed, journalled, file-based storage for biological sequences
A phenotype-based tool for variant prioritization in WES and WGS data
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.
High-level API for storing and querying sequence variant data
VVP (VAAST Variant Prioritizer) rapidly prioritizes genetic variants
provides common tools and lookup tables used primarily by the hgvs and uta packages
[in development] Proof-of-Concept variation translation, validation, and registration service
Visualize microbial evolution at the SNP level!
Filter a VCF to discard false positive variants
From SNP and structural variant calling to GWAS.
Reporting toolbox for happy output
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
Mapping complex genotypes to phenotypic subclusters
Identification and classification of homopolymeric tracts from reads.
Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
coccinelle notes and exercises