Alternatives and similar repositories for CaVEMaN:

Users that are interested in CaVEMaN are comparing it to the libraries listed below

• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆20Updated 3 weeks ago
• vsbuffalo / snakemake-tutorial
  Snakemake tutorial materials
  ☆18Updated 5 years ago
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆37Updated last year
• fritzsedlazeck / SURVIVOR_ant
  A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
  ☆13Updated 7 years ago
• quinlan-lab / ccr
  Building the constrained coding regions (CCR) model
  ☆16Updated 6 years ago
• HurlesGroupSanger / DeNovoWEST
  ☆21Updated 2 weeks ago
• quinlan-lab / ccrhtml
  A small repo for storing the code for making the files and html for CCRs.
  ☆22Updated 5 years ago
• umccr / driver-analysis
  Workflow for driver events identification across cohorts of tumours
  ☆9Updated 9 months ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 4 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated last month
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆27Updated 2 years ago
• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 4 years ago
• HurlesGroupSanger / indelible
  Structural Variation breakpoint discovery via adaptive learning
  ☆15Updated last year
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 6 years ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 4 years ago
• hmgu-itg / VCF-liftover
  Liftover VCF files
  ☆17Updated 8 years ago
• pughlab / VisCap
  VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…
  ☆22Updated 5 years ago
• ernfrid / diagnose_dups
  A tool to examine duplicate read characteristics in a BAM file
  ☆12Updated 7 years ago
• bergmanlab / ngs_te_mapper
  Software for detecting transposable element insertions from next-generation sequencing data
  ☆14Updated 4 years ago
• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆28Updated 2 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• jbelyeu / unfazed
  Unfazed by genomic variant phasing
  ☆26Updated 10 months ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 3 months ago
• talkowski-lab / rCNV2
  Aggregation and analyses of rare CNVs across diseases
  ☆14Updated 2 years ago
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆17Updated 5 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• dellytools / sansa
  Structural variant VCF annotation, duplicate removal and comparison
  ☆31Updated last month
• bioinform / breakseq2
  BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
  ☆24Updated 9 years ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago