overview

Options

Option	Description	Argument
--samples	Sample names. It determines the plotting order If “NA” all samples are used [default NA]	[char …]
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/overview]	[char]
--chrs	Chromosomes to use. If “NA” it uses the same chromsomes as GIP [default NA]	[char …]
--regions	Bed3 file with regions of interest. Regions must be included in –chrs. If "NA" the regions output is not produced [default NA]	[chr]
--MAPQ	Label bins with MAPQ < –MAPQ [default 0]	[int]
--ploidy	Genome ploidy. After normalization multiply coverage values by –ploidy [default 2]	[int]
--highLowCovThresh	Provide two numbers. Bins with normalized coverage values > num1 or < num2 will be labeled [default 1.5 0.5]	[double]
--minDelta	Remove genes with normalized coverage delta < –minDelta [default 0]	[double]
--ylim	Plot visualization threshold. Bin or gene normalized coverage values > –ylim are shown as –ylim [default 5]	[double]
--ylimInt	Bin scatterplot y-axis values interval. If "NA" it is automatically assigned [default NA]	[double]
--maxGe	Plot visualization threshold. Max number of genes to show (ordered by delta coverage) [default 10000]	[int]
--binPlotDim	Bin coverage plot height and width values [default 10 20]	[double double]
--gePlotDim	Gene coverage plot height and width values [default 10 20]	[double double]
--chrPlotDim	Chromosome coverage plot height and width values [default 10 20]	[double double]
--regPlotDim	Regions of interest plot height and width values [default 10 20]	[double double]
--noBin	Omit bin coverage output
--debug	Dump session and quit
-h, --help	Show help message

Description

The overview module aims at comparing the samples in terms of chromosomes, genomic bins and genes sequencing coverage. Unlike other modules like binCNV or geCNV where normalization accounts for chromosome copy number, data in overview is normalized by median genome coverage only. overview is suited to display CNV variation in multiple samples with respect to the reference genome. overview does not perform sequencing coverage ratios between samples. The normalized scores do not represent somy scores. The normalization procedure is such that the coverage of most genomic bins will be centered on 1. The --ploidy parameter can be used to indicate the organism ploidy level, which is 2 by default (diploid). overview multiplies the normalized coverage scores of bins, genes and chromosomes by the ploidy value.

Example

From the GIP worked example folder execute

giptools overview

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

The output consists of five files:

• The .chrCov.pdf file represents the normalized chromosome coverage

• The .binCov.pdf file represents the normalized genomic bin coverage

• The .geCov.pdf file represents the normalized gene coverage. The first heatmap reports scaled values. Genes with 0 standard deviation cannot be scaled and are not shown in the hetmap. The second heatmap shows all the normalized gene coverages increased by a pseudocount of 0.1 and log2 transformed. The third heatmap shows the actual normalized gene coverage, but values greather than –ylim are reported as –ylim.

• The .geCov.xlsx file is an excel table reporting the normalized gene coverage with the associated function (if available)

• The .alignmentMetrics.xlsx is an excel table reporting the mapping statistics of all samples as estimated by picard CollectAlignmentSummaryMetrics.

In the genomic bins plot is possible to center the coverage to 1, limit the y-axis to 2.5 and remove bin coloring by adding the options --ploidy 1 --ylim 2.5 --highLowCovThresh 100 -1 to the command. This gives the following plot:

The options --highLowCovThresh 1.25 0.5 --MAPQ 50 can be used to color the genomic bins with normalized coverage above 1.25 and to label low MAPQ bins:

Optionally providing to regions parameter file with genomic coordinates in Bed3 format (i.e. chromosome<Tab>start<Tab>end), the user can zoom on specific regions of interest (.binCovRegions.pdf output)