panel

Options

Option	Description	Argument
--samplesList	File with a column named “sampleId” listing samples names, plus two TSV columns specifying respectively sample sets and colors [required]	[char]
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/panel]	[char]
--panel	File with three columns named “gene_id”, “set” and “color” listing respectively the gene ID, the panel group, and the color [required]	[char]
--addBackground	Number of random non-panel genes to be added and shown in scatterplots. If “all” all non-panel genes are added. If “none” no genes are added [default none]	[int| “all”|”none”]
--covNorm	Plot gene coverage normalized by [chromosome|genome] median coverage[default genome]	[“chromosome”| “genome”]
--covPlotDim	Gene coverage plot height and width values [default 10 20]	[double double]
--varPlotDim	Gene variants plot height and width values [default 10 20]	[double double]
--contrast	Compare samples from these two sets. If “NA” all samples are considered from the same set [defaul NA]	[char char]
--debug	Dump session and quit
-h, --help	Show help message

Description

The panel module aims at extracting and summarizing the normalized coverage and synonimous (S) and non-synonimous (N) SNV information for one or more gene panels in one or more sample sets. The gene panels are specified with the --panel parameter. The sample sets are specified with the --sampleList parameter. Optionally the use can compare N, S and coverage statistics in two sample sets of interest by specifying the set names with the --contrast parameter.

Example

From the GIP worked example folder execute

giptools panel --sampleList sampleList.tsv --panel panel.tsv

This will generate the panel output files in the gipOut/sampleComparison folder.

The sampleList.tsv is a Tab Separated Value table like this.

The panel.tsv is a separate Tab Separated Value table listing a panel of genes of interest, in this example 68 amastin genes.

The output consists of three files:

• The .coverage.pdf file includes multiple plots showing the sequencing coverage of the genes in the panel normalized by median genomic coverage

• The .variants.pdf file represents the counts of N and S mutations for each gene in the panel

• The panel.xlsx file is an excel table reporting the normalized coverage, the N and S counts for each gene.

For example, one of the coverage plot produced shows the distribution of coverage for each gene (boxes) together with the coverage in individual samples (dots) colored by sample set (first-episode vs relapse infection in this example):

The .variants.pdf file offers alternative visualizations of the N and S mutations. For instance, a stacked barplot showing the mean N and S counts for each gene: