binCNV

Options

Option	Description	Argument
--samples	Two sample names. The ratio is computed Sample2/Sample1 [required]	[char,char]
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/binCNV]	[char]
--chrs	Chromosomes to use. If “NA” it uses the same chromsomes as GIP [default NA]	[char …]
--MAPQ	Label bins with MAPQ < –MAPQ [default 0]	[int]
--ylim	Plot visualization threshold. Bin ratio values greather than this threshold are shown as –ylim [default 3]	[double]
--highLowRatio	Provide 2 numbers. Bins with ratio scores > num1 or < num2 will be colored differently [default 1.5 0.5]	[double,double]
--pseudocount	Normalized mean coverage pseudo count value preventing infinite (1/0) and NaN (0/0) ratio values [default 0.1]	[double]
--debug	Dump session and quit
-h, --help	Show help message

Description

The binCNV module aims at comparing the bin sequencing coverage of 2 samples. This module is useful to identify intra-chromosomal CNV regions between 2 isolates.

For each sample the module loads the GIP files with the bin sequencing coverage (.covPerBin.gz files) and calculates the ratio of the normalized coverage value between corresponding bins.

Example

From the GIP worked example folder execute

giptools binCNV --samples ZK43 LIPA83 --highLowRatio 1.25 0.75

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

The output represents the LIPA83/ZK43 genomic bin normalized coverage ratio, and consists in four files.

The binCNV.overview.pdf file shows the bin coverage ratio of all chromosomes in a row

The binCNV.multiPanel.pdf file shows the bin coverage ratio of all chromosomes in multiple panels

The binCNV.byChr.pdf file contains multiple plots, on for each chromsome separatelly. As an example, the plot produced for chromosome 33 is the following:

The binCNV.xlsx file reports for each genomic bin the genomic coordinates, the computed ratio value and the color used for its representation.