Alternatives and similar repositories for svtools

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

• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated 3 weeks ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 4 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆171Updated last year
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆99Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆202Updated 4 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆103Updated last month
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆159Updated 7 months ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆194Updated this week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated last year
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆170Updated last year
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• gymreklab / GangSTR
  A tool for profiling long STRs from short reads
  ☆99Updated 4 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated last week
• statgen / bamUtil
  ☆91Updated 3 years ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆274Updated 4 months ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆222Updated 8 months ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆75Updated 6 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆90Updated 3 weeks ago