CampagneLaboratory / variationanalysisLinks
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.
☆51Updated 7 years ago
Alternatives and similar repositories for variationanalysis
Users that are interested in variationanalysis are comparing it to the libraries listed below
Sorting:
- Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity☆40Updated 8 years ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆53Updated 8 years ago
- ☆50Updated 6 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 5 years ago
- A simple neural network for calling het-/hom-variants from alignments of single molecule reads to a reference☆59Updated 7 years ago
- ☆54Updated 5 years ago
- De novo assembly based variant calling pipeline for Illumina short reads☆108Updated 4 years ago
- Multi-sample somatic variant caller☆52Updated 3 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 6 years ago
- This repository contains a list of tools or methods that have been used in GIAB analysis☆30Updated 5 years ago
- Method for detecting STR expansions from short-read sequencing data☆63Updated 3 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆51Updated 3 years ago
- ☆69Updated 3 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications☆89Updated 11 months ago
- Support Vector Structural Variation Genotyper☆58Updated 5 years ago
- Flexible genotype query among 30,000+ samples whole-genome☆94Updated 6 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆98Updated 3 years ago
- Tools for early stage alignment file processing☆95Updated 6 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆49Updated 6 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 8 years ago
- Exon-exon splice junctions across SRA☆42Updated 4 years ago
- phenotype-based prioritization of candidate genes for human diseases☆65Updated 2 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Updated 4 years ago
- Annotate models of genetic inheritance patterns in variant files (vcf files)☆84Updated last month
- Kart: A divide-and-conquer algorithm for NGS read mapping with high error tolerance☆26Updated 5 years ago
- NuDup -- Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.☆14Updated 5 years ago
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆112Updated 2 years ago
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 6 years ago
- Python module for the easy handling and analysis of DNase-seq data☆37Updated 6 years ago