Alternatives and similar repositories for vt

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

• AstraZeneca-NGS / VarDict
  VarDict
  ☆200Updated last year
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆137Updated 4 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 3 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆133Updated 4 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last week
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆318Updated last week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆161Updated 9 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated 2 weeks ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆137Updated last week
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆241Updated 7 months ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆158Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆258Updated 3 months ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆153Updated 2 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆223Updated 3 years ago
• shiquan / bamdst
  a lightweight bam file depth statistical tool
  ☆150Updated 8 months ago
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆97Updated 6 months ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆168Updated 5 years ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆156Updated 2 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆137Updated 5 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated 2 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated last year
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆148Updated last week
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆252Updated 11 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆188Updated last week