genome / analysis-workflows

Related projects: ⓘ

• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆187Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆141Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆146Updated 3 weeks ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆131Updated last year
• CCDG / Pipeline-Standardization
  ☆81Updated 5 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆137Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆122Updated 3 months ago
• broadinstitute / gatk-docs
  Documentation archive for GATK tools and workflows
  ☆82Updated 4 years ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆106Updated 3 years ago
• biowdl / tasks
  A collection of reusable WDL tasks. Category:Other
  ☆85Updated 3 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆169Updated this week
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆90Updated 4 months ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆94Updated 2 years ago
• nf-core / raredisease
  Call and score variants from WGS/WES of rare disease patients.
  ☆83Updated last week
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆133Updated 3 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆210Updated 2 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆187Updated 8 months ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆137Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆93Updated 3 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆153Updated 2 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…
  ☆50Updated 3 years ago
• SciLifeLab / Sarek
  Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
  ☆132Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆152Updated last year
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆92Updated 3 months ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆137Updated 5 months ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆71Updated 3 months ago
• mozack / abra2
  ABRA2
  ☆90Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆68Updated 3 years ago
• EGA-archive / ega-download-client
  A Python-based EGA download client
  ☆93Updated 5 months ago
• broadinstitute / cromshell
  CLI for interacting with Cromwell servers
  ☆53Updated 5 months ago