Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
☆31Apr 19, 2018Updated 8 years ago
Alternatives and similar repositories for varscan2
Users that are interested in varscan2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆166Mar 28, 2023Updated 3 years ago
- Variant quality checking scripts.☆12Feb 4, 2016Updated 10 years ago
- An R package to create a pretty Copy Number Variant plot from a segments file☆11Feb 25, 2025Updated last year
- call copy number from WES(WXS)☆12May 10, 2021Updated 5 years ago
- VarDict☆204Jan 5, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆35Sep 28, 2020Updated 6 years ago
- 📊Evaluating, filtering, comparing, and visualising VCF☆29Mar 9, 2023Updated 3 years ago
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆179Jan 7, 2020Updated 6 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆20Jul 6, 2026Updated 3 months ago
- Bioconductor components for general cancer genomics☆11Feb 5, 2023Updated 3 years ago
- ☆17Dec 29, 2025Updated 9 months ago
- ☆44Nov 18, 2019Updated 6 years ago
- An ensemble approach to accurately detect somatic mutations using SomaticSeq☆207Aug 23, 2026Updated last month
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆421May 25, 2026Updated 4 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)☆15Nov 5, 2020Updated 5 years ago
- Probabilistic model for inferring clonal population structure from deep NGS sequencing.☆127Aug 19, 2020Updated 6 years ago
- Website for the precision medicine workshop☆49Updated this week
- Causal Variant Evidence Mapping with Non-parametric resampling☆12Dec 16, 2020Updated 5 years ago
- Bayesian genotyper for structural variants☆137Apr 13, 2026Updated 6 months ago
- ClairS-TO - a deep-learning method for tumor-only somatic variant calling☆98Sep 9, 2026Updated last month
- Machine learning use cases for teaching☆13Jul 12, 2017Updated 9 years ago
- GTEx analysis scripts☆20Mar 14, 2017Updated 9 years ago
- CAVA (Clinical Annotation of VAriants)☆14Sep 28, 2018Updated 8 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- development of network co-localization tool☆18Sep 21, 2026Updated 3 weeks ago
- software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis☆31Jan 24, 2022Updated 4 years ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆151Sep 9, 2020Updated 6 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Oct 26, 2018Updated 7 years ago
- Genomic variant annotation and functional effect prediction☆313Mar 9, 2026Updated 7 months ago
- Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi☆21Jan 28, 2025Updated last year
- Codes to regenerate figures for mutagen paper☆12Apr 8, 2021Updated 5 years ago
- ☆18Aug 22, 2021Updated 5 years ago
- Terraform template to create AWS resources to execute jobs using nextflow☆22Mar 1, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- 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…☆44Aug 24, 2022Updated 4 years ago
- A Weighted Exact Test for Mutually Exclusive Mutations in Cancer☆20Sep 30, 2018Updated 8 years ago
- microsatellite instability detection using tumor only or paired tumor-normal data☆133Jan 6, 2021Updated 5 years ago
- ☆19Jun 11, 2025Updated last year
- Nanopanel2: a somatic variant caller for Nanopore panel sequencing data☆11Sep 21, 2021Updated 5 years ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆24Mar 20, 2026Updated 6 months ago
- Snakemake based pipeline for RNA-Seq analysis☆31Jun 26, 2019Updated 7 years ago