broadinstitute / oncotator
☆68Updated 2 years ago
Alternatives and similar repositories for oncotator:
Users that are interested in oncotator are comparing it to the libraries listed below
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 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
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆98Updated 2 years ago
- ☆41Updated last year
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- ☆57Updated 5 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Updated 4 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆56Updated 4 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 6 years ago
- Concordance and contamination estimator for tumor–normal pairs☆58Updated 6 months ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆53Updated 7 years ago
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- Characterization of Germline variants☆98Updated 3 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Genomes on the Cloud, Mapping & Variant Calling Pipelines☆34Updated 8 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- An awk-like VCF parser☆56Updated last year
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 2 months ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- Reference data: BED files, genes, transcripts, variations.☆83Updated 7 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆50Updated 2 years ago
- Relevant papers for CNV and SV approaches☆94Updated 6 months ago
- Galaxy RNA workbench☆40Updated 4 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 8 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
- Tumor Mutational Burden☆58Updated 8 months ago
- Burden testing against public controls☆50Updated last year