Alternatives and similar repositories for broad-prod-wgs-germline-snps-indels

Users that are interested in broad-prod-wgs-germline-snps-indels are comparing it to the libraries listed below

• 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
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 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
  ☆56Updated 5 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆71Updated 7 years ago
• broadinstitute / oncotator
  ☆68Updated 3 years ago
• molgenis / NIPTeR
  R Package for Non Invasive Prenatal Testing (NIPT) analysis
  ☆41Updated 5 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated 10 months ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆60Updated 8 months ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆69Updated last week
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆66Updated 2 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 8 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 11 months ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 2 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆73Updated 5 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆134Updated last year
• ikalatskaya / ISOWN
  ☆46Updated 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…
  ☆22Updated 2 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• Kennedy-Lab-UW / Duplex-Seq-Pipeline
  A standalone end-to-end data analysis pipeline for Duplex Sequencing
  ☆20Updated last year