AlexandrovLab / EnsembleVariantCallingPipeline
The EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers (Mutect2, Strelka2, Varscan2, MuSE) and indel variant calling from 3 variant callers (Mutect2, Strelka2, Varscan2).
☆13Updated last year
Alternatives and similar repositories for EnsembleVariantCallingPipeline:
Users that are interested in EnsembleVariantCallingPipeline are comparing it to the libraries listed below
- hands-on for NGS/SNParray CNV call trainning☆17Updated 2 years ago
- DriverPower☆26Updated last month
- Filter and prioritize fusion calls☆20Updated 4 months ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆20Updated 3 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- ☆11Updated 4 months ago
- Workflow for Sequenza, cellularity and ploidy☆19Updated 7 months ago
- Codes and Data for FFPEsig manuscript☆15Updated last year
- Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and …☆12Updated 2 weeks ago
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- ☆23Updated 3 years ago
- ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…☆11Updated 3 months ago
- DRAGEN Tumor/Normal workflow post-processing☆22Updated last year
- R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…☆16Updated 4 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Updated 3 years ago
- ☆11Updated last year
- SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…☆19Updated 2 weeks ago
- CNAqc - Copy Number Alteration (CNA) Quality Check package☆19Updated 3 months ago
- ☆10Updated 4 years ago
- GENome Organisation Visual Analytics☆15Updated 3 years ago
- Allele-Specific Expression by Single-Cell RNA Sequencing☆28Updated 4 years ago
- CNV analysis workflow code for the manuscript☆13Updated 4 years ago
- A flexible framework to annotate and prioritize cancer somatic mutations.☆8Updated 7 years ago
- Code and files accompanying article "The landscape of somatic mutation in normal colorectal epithelial cells"☆11Updated 3 years ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Updated 5 years ago
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 5 months ago
- RNA-seq workflow: differential transcript usage☆20Updated last year
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 2 months ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆15Updated last year
- ☆13Updated 7 years ago