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 GRCh38, supports GRCh37 and T2T via liftover
• Supports multiallelic variants
• Short variant detection
• Structural variant detection
• Short tandem repeat detection
• Copy number variant detection (Oxford Nanopore, PacBio HiFi)
• Consequence aware
• Rich set of variant annotations
• Pathogenic variant prioritization (CAPICE)
• Phenotype support (HPO v2024-08-13)
• Inheritance matching (VIP inheritance matcher)
• Variant classification and filtration using customizable decision trees
• Variant reporting using customizable report templates
• Quick reanalysis