Alternatives and similar repositories for VarDictJava:

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

• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆195Updated 3 years ago
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆122Updated last year
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆134Updated 3 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆237Updated 4 months ago
• shiquan / bamdst
  a lightweight bam file depth statistical tool
  ☆149Updated 5 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆179Updated this week
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆150Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆266Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆120Updated 3 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆128Updated 8 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆96Updated 9 months ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆175Updated 9 months ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆174Updated 2 months ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆128Updated 4 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆237Updated last month
• pcingola / SnpEff
  ☆263Updated last week
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆82Updated 2 weeks ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• hartwigmedical / hmftools
  Various algorithms for analysing genomics data
  ☆210Updated this week
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• OpenGene / gencore
  Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
  ☆116Updated last year