cnv_caller.py

Python script to call copy number variations from platform independent NGS data

Usage: cnv_caller.py [options]

Options: -h, --help

                    show this help message and exit

-w INT, --windowSize=INT

                    Windowsize (bp) to be used to calculate log2ratio
                    [Default:500]

-m INT, --mappingQuality=INT

                    Mapping quality cutoff for reads to be used in the
                    calculation [Default:0]

-f FILE, --file=FILE

                    Input bam file to be analyzed, should be sorted and
                    indexed

-o PATH, --ouput=PATH

                    Output path

-l FILE, --name-list=FILE

                    List of bam headers in order as they should be
                    plotted, [Default:/Users/Simon/git/CNV_pipe/chr.list]

-a BOOLEAN, --plot=BOOLEAN

                    pecify if plotting should be done using DNAcopy
                    [Default:True]

-r FILE, --reference=FILE

                    Bam file to be used as refernce / control

Developed by: Simon Stenberg

Dependencies

pysam (install: pip install pysam)

R (developed in R version 3.1.0 (2014-04-10) -- "Spring Dance")

R library DNAcopy http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html

Install

Clone repo and go!

Preceeding data handling

• You need at least 1 set of reads aligned to a reference genome/contigs
• Preferably use a refrence alignment of to compare with, for example ancestral genome (reference) vs evolved genome (sample)
• Bam files must be sorted and indexed
• Preferably use some kind of GC-correction. Deeptools is one example that can do this.

Caveats

Things to know about algorithm

• Minimal reference coverage assumed at each base for the reference = 1

• Without reference log2ratio is calculated with chromosome median coverage

• Headers in both bams need to be identical

• Output path does not have to exist, it will be created if it can be

• List the bam headers (chromosome names) in a list to specify the order of chromosomes in plot. Example is included in repo (chr.list)