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
- 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
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- ☆38Updated last year
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆96Updated 3 years ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆56Updated 3 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Concordance and contamination estimator for tumor–normal pairs☆57Updated 3 months ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 4 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- CNV screening and annotation tool☆24Updated 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
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Genomes on the Cloud, Mapping & Variant Calling Pipelines☆33Updated 7 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 4 years ago
- Reference data: BED files, genes, transcripts, variations.☆82Updated 7 years ago
- ☆45Updated 5 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- Identifying recurrent mutations in cancer☆37Updated 3 years 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
- ☆66Updated last year
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- Relevant papers for CNV and SV approaches☆94Updated 3 months ago
- Galaxy RNA workbench☆39Updated 4 years ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆76Updated 2 months ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆75Updated last year
- ☆52Updated 2 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆43Updated 2 years ago