Alternatives and similar repositories for gatk4-somatic-cnvs

Users that are interested in gatk4-somatic-cnvs are comparing it to the libraries listed below

• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆131Updated last year
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 7 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆37Updated 3 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆68Updated 3 weeks ago
• OSU-SRLab / MANTIS
  Microsatellite Analysis for Normal-Tumor InStability
  ☆76Updated 3 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆62Updated 3 months ago
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 2 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• RahmanTeam / DECoN
  ☆54Updated 2 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆52Updated last year
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆113Updated 6 months ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated last year
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• gatk-workflows / gatk3-4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
  ☆54Updated 5 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆110Updated last year
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆52Updated 3 years ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆78Updated last year