broadinstitute / oncotator
☆67Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for oncotator
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- 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
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆76Updated 4 years ago
- R package for inferring copy number from read depth☆31Updated 2 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆55Updated 3 years ago
- ☆38Updated 9 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- QDNAseq package for Bioconductor☆48Updated 3 months ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- Reference data: BED files, genes, transcripts, variations.☆81Updated 6 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- CNV screening and annotation tool☆24Updated 8 years ago
- identifying mutational significance in cancer genomes☆60Updated last year
- Battenberg algorithm and associated implementation script☆51Updated 4 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- An awk-like VCF parser☆54Updated 10 months ago
- A false-positive filter for variants called from massively parallel sequencing☆29Updated 7 years ago
- Concordance and contamination estimator for tumor–normal pairs☆55Updated 2 weeks ago
- Snakemake-based workflow for detecting structural variants in genomic data☆77Updated 8 months ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- ☆50Updated last year
- Phenotype driven gene prioritization for HPO☆44Updated 3 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