PAVplotR

Abstract

PAVplotR is an R package that accepts as input a haploid VCF and, for a user-specified bin size, calculates proportional presence-absence variation (PAV). First, all variants in the file are considered to calculate an expanded coordinate system that accounts for insertions relative to the reference sequence. Next, for each sample in the VCF, proportional PAV is summarized per bin in the expanded coordinate system and finally, PAV is plotted such that rows are samples and columns are bins with the x-axis (chromosome position) labeled according to the reference haplotype's original coordinate system.