ternaryBin

Options

Option	Description	Argument
--samples	Sample names. It determines the plotting order [required]	[char …]
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/ternaryBin]	[char]
--chrs	Chromosomes to use. If “NA” it uses the same chromsomes as GIP [default NA]	[char …]
--minMAPQ	Remove bins with MAPQ < –MAPQ [default 0]	[int]
--pseudocount	Normalized mean coverage pseudocount value (for ternary plot only) [default 0.1]	[double]
--highLowDensityColor	Colors for high and low density [default black deepskyblue]	[char char]
--densityN	Number of grid points in each direction [default 200]	[int]
--densityBins	Number bins over which to calculate intervals [default 8000]	[int]
--showSubset	Show a random subset of genomic bins. Does not affect the density estimation [default 5000]	[int]
--debug	Dump session and quit
-h, --help	Show help message

Description

The ternaryBin module aims at comparing the bin sequencing coverage of 3 samples to identify CNVs regions.

The module loads for the three samples the GIP files with the bin sequencing coverage values (.covPerBin.gz files) and generates a ternary diagram of the normalized coverage values. In this representation, the values coverage values in the 3 samples sum to a constant represented for convenience as 100%. Depending on the genome size the number of bins can be very large. To ease plot readability and lower the CPU requirements this module generates a 2D kernel density estimatation of the data, and materializes just a random subset of genomic bins as dots.

Example

From the GIP worked example folder execute

giptools ternaryBin --samples ZK43 LIPA83 ZK28

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

The user can test different vaules of --densityN and --densityBins to adjust the density area representation. For instance adding to the previous example the parameters --densityN 150 --densityBins 3000 results in the following plot:

The ternaryBin.xlsx file reports for each bin the genomic coordinates, the computed normalized coverage scores, the minimum MAPQ score, the delta coverage and fold change values in the three samples.