Alternatives and similar repositories for pileup2base

Users that are interested in pileup2base are comparing it to the libraries listed below

• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 5 months ago
• mikessh / mageri
  MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
  ☆21Updated 8 years ago
• WGLab / SeqMule
  Automated human exome/genome variants detection from FASTQ files
  ☆22Updated 3 years ago
• jrflab / modules
  MSKCC Reis-Filho Lab pipeline thingy
  ☆17Updated 3 months ago
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 4 years ago
• TranslationalBioinformaticsIGTP / CNVbenchmarkeR
  Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data
  ☆14Updated 8 months ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 5 years ago
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆36Updated 2 years ago
• smped / ngsReports
  ☆23Updated 2 months ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆22Updated last year
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 7 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆28Updated 2 years ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 4 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆35Updated 7 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 3 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆39Updated 4 years ago
• sirselim / diagnostics_exome_reporting
  Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
  ☆14Updated 5 years ago
• ssadedin / ximmer
  Ximmer is a system for CNV calling on exome and targeted genomic sequencing
  ☆19Updated 3 weeks ago
• sdchandra / CNAclinic
  ☆25Updated last year
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆32Updated 6 years ago
• stephenturner / adapters
  Adapters for trimming
  ☆30Updated 6 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• cancerit / cgpBigWig
  BigWig manpulation tools using libBigWig and htslib
  ☆29Updated last year
• guigolab / bamstats
  A command line tool to compute mapping statistics from a BAM file
  ☆24Updated 3 years ago
• dantaki / CNVplot
  Plot CNV data with a genome viewer in R
  ☆15Updated 8 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 7 months ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 5 years ago