Alternatives and similar repositories for gatk4-genome-processing-pipeline

Users that are interested in gatk4-genome-processing-pipeline are comparing it to the libraries listed below

• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆74Updated 4 months ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 9 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 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
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆69Updated 2 years ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆77Updated 7 months ago
• oliverSI / GATK4_Best_Practice
  GATK4 Best Practice Nextflow Pipeline
  ☆33Updated 7 years ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆48Updated 4 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆39Updated 4 years ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆91Updated 2 months 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
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 9 months ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• Illumina / GTCtoVCF
  Script to convert GTC/BPM files to VCF
  ☆47Updated last month
• babelomics / SMAca
  SMN1 copy-number and sequence variant analysis from next generation sequencing data
  ☆23Updated 2 years ago
• 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
• gatk-workflows / five-dollar-genome-analysis-pipeline
  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  ☆57Updated 5 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆52Updated 5 years ago
• BimberLab / DISCVRSeq
  A collection of command line tools for working with sequencing data
  ☆52Updated last week
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆74Updated 6 years ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆73Updated last month
• c-BIG / NPM-sample-qc
  reference implementation of GA4GH WGS Quality Control Standards
  ☆11Updated 3 months ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• Helix-Research-Lab / PGxPOP
  PGxPOP
  ☆17Updated 2 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆55Updated this week
• hartwigmedical / pipeline5
  ☆21Updated last month