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")

Clone repo and go!

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.

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)