CampagneLaboratory / variationanalysis
This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate deep learning models trained with semi-simulation. See docs below for details.
☆50Updated 6 years ago
Alternatives and similar repositories for variationanalysis:
Users that are interested in variationanalysis are comparing it to the libraries listed below
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago
- ☆68Updated 2 years ago
- 3D hotspot mutation proximity analysis tool☆46Updated last year
- Exon-exon splice junctions across SRA☆40Updated 3 years ago
- Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity☆39Updated 7 years ago
- De novo assembly based variant calling pipeline for Illumina short reads☆108Updated 4 years ago
- Read visualizer for structural variants☆81Updated 6 years ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆51Updated 7 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- Fast spliced aligner with low memory requirements☆41Updated 9 years ago
- ☆23Updated 6 years ago
- Visualization and annotation of CNVs from population-scale whole-genome sequencing data☆70Updated 7 years ago
- ☆49Updated 2 years ago
- RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection☆29Updated 4 years ago
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆108Updated 2 years ago
- ☆30Updated 4 years ago
- ☆53Updated 4 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 7 years ago
- This repository contains information about latest release from Genome in a Bottle project☆73Updated 5 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Galaxy RNA workbench☆39Updated 4 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 6 years ago
- Genomes on the Cloud, Mapping & Variant Calling Pipelines☆33Updated 7 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆89Updated 4 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 5 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 2 weeks ago
- Python module for the easy handling and analysis of DNase-seq data☆37Updated 5 years ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆25Updated 8 years ago
- A method to identify structural variation from sequencing data in target regions☆31Updated 4 years ago