breakpoint.finder.interactive: Interactive breakpoint finder

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Interactive tool to fine tune breakpoint location from the BAM files. An interactive Shiny app will open in your web browser. There, the bp coverage of the 'test.sample' will be shown along with the coverage of the reference samples ('ref.samples'). The user can then slide the breakpoint where the tested samples starts to deviate from the reference. If the deviation is not clear a few parameters (e.g. mapping quality, resolution) can be changed live. Once satisfied the user pushes a button and the function returns the new breakpoint locations. In practice this function can be looped over to quickly fine-tune the breakpoints of several CNVs.

Usage

breakpoint.finder.interactive(chr, start, end, test.sample, files.df,
  ref.samples, proper = TRUE, nb.cores = 1, bp.res = 1, flanks = 2000,
  related.samples = NULL)

Arguments

chr	the chromosome
start	the start position
end	the end position
test.sample	the sample with abnormal coverage
files.df	a data.frame with the path to the bam files
ref.samples	other samples to visualize
proper	should proper mapping be counted.
nb.cores	number of cores
bp.res	default resolution (bp)
flanks	default flank size (bp)
related.samples	samples related to the 'test.sample' (e.g. parents) to be drawn in a special color.

Details

Access to the BAM files is necessary, but also to a web-browser (for the application). Hence I would recommend to mount the cluster/server with the BAM on your personnal laptop to use this. Then you might need to tweak a bit the paths in the 'bam' column of 'files.df' to include your mounting location.

Value

a list with

bk.df	a data.frame with the breakpoint coordinates
graph	the ggplot object with the final graph

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.