Alternatives and similar repositories for gatk4-exome-analysis-pipeline

Users that are interested in gatk4-exome-analysis-pipeline are comparing it to the libraries listed below

• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated last year
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆71Updated 11 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆108Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 9 months ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆101Updated this week
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• hartwigmedical / pipeline5
  ☆21Updated last week
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆43Updated last year
• parklab / ShatterSeek
  ☆71Updated 2 years ago
• naumanjaved / fingerprint_maps
  Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…
  ☆28Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• girirajanlab / CN_Learn
  CN-Learn
  ☆29Updated 5 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆84Updated 7 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆134Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 3 weeks ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆74Updated 11 months ago
• iprada / Circle-Map
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads
  ☆65Updated last year