ivg_sv: Interactive exploration of SVs in a variation graph

In jmonlong/sveval: SV evaluation

Interactive exploration of SVs in a variation graph

Description

Opens a Shiny app with a dynamic table that contains input SVs. Clicking on a SV (row in the table) generates a simplified representation of the variation graph around this SV. The number of flanking nodes (context) can be increased if necessary, e.g. for large insertions. vg needs to be installed (https://github.com/vgteam/vg).

Usage

ivg_sv(svs, xg, ucsc.genome = "hg38")

Arguments

svs	either a GRanges with SVs (e.g. from readSVvcf) or the path to a VCF file.
xg	the path to the xg object of the variation graph.
ucsc.genome	the genome version for the UCSC Genome Browser automated link.

Value

Starts a Shiny app in a web browser.

Author(s)

Jean Monlong

jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.