genome / somatic-sniper
A tool to call somatic single nucleotide variants.
☆40Updated 9 years ago
Related projects ⓘ
Alternatives and complementary repositories for somatic-sniper
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- A false-positive filter for variants called from massively parallel sequencing☆29Updated 7 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- identifying mutational significance in cancer genomes☆60Updated last year
- ☆67Updated 2 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
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- Gene Fusion Visualiser☆51Updated last year
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- ☆45Updated 4 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
- A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …☆60Updated 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- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
- for visual evaluation of read support for structural variation☆49Updated 5 months ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆51Updated 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 PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 4 years ago
- 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
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 4 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Concordance and contamination estimator for tumor–normal pairs☆55Updated 2 weeks ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Mutation Identification Pipeline. Read the latest documentation:☆44Updated 8 months ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated 2 weeks ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆55Updated 3 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆77Updated 8 months ago
- Kourami: Graph-guided assembly for HLA alleles☆35Updated 5 years ago
- Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets☆37Updated 4 years ago