Alternatives and similar repositories for transvar

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

• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 11 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated last week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆170Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆135Updated last year
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆185Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated this week
• AstraZeneca-NGS / VarDictJava
  VarDict Java port
  ☆135Updated last year
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated last month
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆135Updated 2 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆194Updated this week
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆204Updated 4 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆203Updated last year
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 3 weeks ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆201Updated 4 years ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆116Updated 9 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated last week
• imgag / ngs-bits
  Short-read and long-read sequencing tools for diagnostics
  ☆165Updated this week
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 10 months ago