Alternatives and similar repositories for PennCNV2

Users that are interested in PennCNV2 are comparing it to the libraries listed below

• vpc-ccg / svict
  Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
  ☆29Updated last year
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 5 years ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 5 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years ago
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆31Updated 2 months ago
• danielfan / MuSE
  Somatic point mutation caller
  ☆17Updated 9 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 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
• sdchandra / CNAclinic
  ☆26Updated last year
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 5 years ago
• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆23Updated 3 months ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆29Updated 4 years ago
• talkowski-lab / svtk
  ☆35Updated 4 years ago
• broadinstitute / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆25Updated 9 years ago
• ExpressionAnalysis / HLAProfiler
  Using k-mers to call HLA alleles in RNA sequencing data
  ☆23Updated 7 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 7 months ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆23Updated 2 years ago
• jcarrotzhang / LoLoPicker
  picking up low allelic-fraction, somatic variants from tumor samples
  ☆14Updated 7 years ago
• talkowski-lab / gnomad-sv-pipeline
  Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
  ☆36Updated 5 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 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
• sigven / vcf2tsvpy
  Genomic VCF to tab-separated values
  ☆47Updated 2 years ago
• polyactis / Accucopy
  Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…
  ☆17Updated last year
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• gedoardo83 / GARFIELD-NGS
  GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS
  ☆17Updated 6 years ago
• vpc-ccg / calib
  Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.
  ☆39Updated 2 years ago