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Key features

VIP is an easy to install, easy to use, portable and flexible pipeline implemented using Nextflow. Features include:

  • Workflows for a broad range of input file types: bam, cram, fastq, g.vcf, vcf
  • Produces stand-alone variant interpretation HTML report with integrated genome browser
  • Long-read sequencing support (Oxford Nanopore, PacBio HiFi)
  • Short-read sequencing support (Illumina, both single and paired-end reads)
  • Supports GRCh37 and GRCh38
  • Short variant detection
    • Limitation: VIP currently does not support short variant detection on Mitochondrial DNA
  • Structural variant detection
  • Consequence-agnostic
  • Rich set of variant annotations
  • Pathogenic variant prioritization (CAPICE)
  • Phenotype support (HPO)
  • Inheritance matching (VIP inheritance matcher)
  • Variant classification and filtration using customizable decision trees
  • Variant reporting using customizable report templates
  • Quick reanalysis