Alternatives and similar repositories for mutect

Users that are interested in mutect are comparing it to the libraries listed below

• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆111Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated last month
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• morrislab / phylowgs
  Application for inferring subclonal composition and evolution from whole-genome sequencing data.
  ☆111Updated 3 years ago
• 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated 2 years ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆87Updated 7 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆108Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• raphael-group / THetA
  Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberration…
  ☆73Updated 4 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆205Updated last year
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆110Updated last year
• konradjk / loftee
  ☆182Updated 2 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆132Updated last year
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆114Updated 6 years ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• vals / umis
  Tools for processing UMI RNA-tag data
  ☆131Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆95Updated 4 years ago