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

• Clinical-Genomics / stranger
  Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
  ☆32Updated last week
• 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
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆47Updated this week
• GeneDx / scramble
  ☆39Updated last year
• 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 PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆55Updated 5 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated 9 months 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…
  ☆53Updated 4 years ago
• ryanlayer / stix
  Structural Variant Index
  ☆74Updated 6 months ago
• babelomics / SMAca
  SMN1 copy-number and sequence variant analysis from next generation sequencing data
  ☆23Updated 2 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆73Updated 5 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆77Updated last year
• Illumina / SMNCopyNumberCaller
  A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS
  ☆49Updated 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.
  ☆70Updated 3 weeks ago
• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆46Updated 4 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆66Updated 2 years ago
• Illumina / Polaris
  Data and information about the Polaris study
  ☆53Updated 5 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 2 years ago
• talkowski-lab / svtk
  ☆35Updated 4 years ago
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 3 years ago
• fakedrtom / SVAFotate
  ☆41Updated 9 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 4 months ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆48Updated 2 years ago
• jzook / genome-data-integration
  Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls
  ☆44Updated 3 years ago