Alternatives and similar repositories for varscan2

Users that are interested in varscan2 are comparing it to the libraries listed below

• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆31Updated 3 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• kylessmith / SomVarIUS
  Somatic variant identification from unpaired samples
  ☆15Updated 8 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 3 years ago
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 2 years ago
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆44Updated 2 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆54Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 10 months ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 5 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆28Updated 3 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 6 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 9 months ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 2 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 3 months ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• GeneDx / scramble
  ☆39Updated last year
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 3 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆33Updated 9 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆53Updated last month
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆50Updated 3 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 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