Alternatives and similar repositories for gatk4-GenotypeGVCFs-nf

Users that are interested in gatk4-GenotypeGVCFs-nf are comparing it to the libraries listed below

• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆28Updated 2 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…
  ☆26Updated last month
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 3 months ago
• Phillip-a-richmond / AnnotateVariants
  This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions …
  ☆17Updated 2 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆35Updated last year
• asntech / QDNAseq.hg38
  QDNAseq bin annotation for hg38
  ☆15Updated 2 months ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆34Updated 8 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…
  ☆53Updated 4 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 3 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• biocore-ntnu / snpflip
  Report reverse and ambiguous strand SNPs in GWAS data
  ☆33Updated 6 years ago
• hartwigmedical / pipeline5
  ☆21Updated this week
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆45Updated 2 years ago
• QingliGuo / FFPEsig
  Codes and Data for FFPEsig manuscript
  ☆17Updated last year
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• alkodsi / ctDNAtools
  R package to work with ctDNA sequencing data
  ☆40Updated 3 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• babelomics / SMAca
  SMN1 copy-number and sequence variant analysis from next generation sequencing data
  ☆23Updated 2 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• eyzhao / hrdetect-pipeline
  ☆34Updated 5 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• AlexandrovLab / SigProfilerSingleSample
  SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity…
  ☆23Updated 4 months ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 9 months ago
• parklab / ShatterSeek
  ☆69Updated last year