Alternatives and similar repositories for gatk3-4-rnaseq-germline-snps-indels

Users that are interested in gatk3-4-rnaseq-germline-snps-indels are comparing it to the libraries listed below

• gatk-workflows / gatk4-somatic-cnvs
  This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organi…
  ☆44Updated 5 years ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆77Updated last year
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆60Updated 5 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• FusionInspector / FusionInspector
  FusionInspector code
  ☆58Updated 3 months ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• alkodsi / ctDNAtools
  R package to work with ctDNA sequencing data
  ☆45Updated 3 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 6 months ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆94Updated 8 years ago
• heathsc / gemBS
  gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…
  ☆32Updated 3 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆99Updated 4 years ago
• parklab / SigMA
  Mutational signature analysis for low statistics SNV data
  ☆64Updated last year
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• OpenGenomics / mc3
  ☆35Updated 5 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆83Updated 11 months ago
• nghiavtr / FuSeq
  ☆33Updated 3 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• BIMSBbioinfo / genomation
  R package for genomic feature analysis and visualization
  ☆79Updated 8 months ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆87Updated this week
• hellbelly / BS-Snper
  ☆39Updated 4 years ago