umccr / vcf_stuff
πEvaluating, filtering, comparing, and visualising VCF
β27Updated 2 years ago
Alternatives and similar repositories for vcf_stuff:
Users that are interested in vcf_stuff are comparing it to the libraries listed below
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variationsβ29Updated 6 years ago
- An R package for predicting HR deficiency from mutation contextsβ28Updated 2 months ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencingβ37Updated 3 years ago
- DriverPowerβ26Updated 3 months ago
- a parallel R package for detecting copy-number alterations from short sequencing readsβ23Updated 3 years ago
- β34Updated 5 years ago
- VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number vaβ¦β22Updated 5 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needsβ30Updated last year
- Utility functions for FACETSβ35Updated last year
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated maβ¦β49Updated 2 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signaturesβ60Updated 5 years ago
- β46Updated 5 years ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.β28Updated 6 years ago
- Joint calling of gVCF, following GATK4 Best Practicesβ12Updated 6 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNAβ27Updated 4 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.β32Updated 8 years ago
- a set of NGS pipelinesβ24Updated 2 weeks ago
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variantsβ22Updated 5 years ago
- β13Updated 7 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomesβ26Updated 6 years ago
- A set of tools to annotate VCF files with expression and readcount dataβ29Updated last month
- This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions β¦β17Updated 2 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2β29Updated 7 years ago
- Filters for false-positive mutation calls in NGSβ30Updated 6 years ago
- Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data setsβ37Updated 4 years ago
- DRAGEN Tumor/Normal workflow post-processingβ22Updated last year
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analysesβ31Updated 3 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq dataβ42Updated 3 years ago
- highly-efficient & lightweight mutation signature matrix aggregationβ19Updated 3 years ago
- MSKCC Reis-Filho Lab pipeline thingyβ17Updated 8 months ago