AMYCNE

AMYCNE is a copy number estimation toolkit, designed for WGS data. It contains modules for genotyping of copy number, counting the number of chromosomes, annotating vcf files, and calling CNVs. AMYCNE require coverage tab files as input, these files may e produced using TIDDIT.

NOTE: The variant calling module is in a development stage, use it at your own risk!

Installation

AMYCNE requires bottleneck, scipy and numpy. These two packages may be installed using pip:

pip install numpy
pip install scipy
pip install bottleneck

AMYCNE has been tested on python 2.7.11, but might run on older versions of python as well. To improve the performance of AMYCNE, the code of AMYCNE may be compiled using cython:

python setup.py build_ext --inplace

Run

Type the following for a list of modules:

python AMYCNE.py

The following section decribes the basic commands for running AMYCNE, for more info, use the --help flag for each module. Each module requires a coverage file and a gc content file, having the same bin size.

Genotype: estimate the copy number in one or more target region
  Use the genotype module by typing:
    python AMYCNE.py --genotype
    
  Use the following command to genotype a specified region(chr1:100-10000):
  python AMYCNE.py --genotype --gc GC_tab_file.tab --coverage coverage_tab_file.tab --R chr1:100-10000
  
  To genotype all coverage files in a folder type the followin command:
  python AMYCNE.py --genotype --gc GC_tab_file.tab --folder /path/to/folder --R chr1:100-10000
  
  Multiple regions could be genotyped using a region text file instead of the --R flag:
  python AMYCNE.py --genotype --gc GC_tab_file.tab --coverage coverage_tab_file.tab --region region.txt
  python AMYCNE.py --genotype --gc GC_tab_file.tab --folder /path/to/folder --region region.txt
  
The region file consists of operations. Each line within the region text file describes one operation. THe supported operations are sum(sum) and average(avg). The operations are written in the following format:

sum(1:104198143-104207173|1:104230040-104238912|1:104292279-104301311)
avg(1:104198143-104207173|1:104230040-104238912|1:104292279-104301311)

Each region is separated by |, any number of regions within one operation is supported(except 0), and any number of operations within a region file is allowed.

Anotate: estimate the copy number across structural variants stored in a vcf file
    Use the anotate module by typing:
      python AMYCNE.py --anotate
      
    The annotate module requires a coverage file, a gc content file, as well as the structural variant vcf:
     python AMYCNE.py --anotate --gc gc_content_file.tab --coverage coverage.tab --vcf sv.vcf > annotated.sv.vcf

Call: Perform CNV calling
  Use the call module by typing:
      python AMYCNE.py --call
      
  The call module requires a coverage file, and a gc content file, and prints vcf file to --output
     python AMYCNE.py --call --gc gc_content_file.tab --coverage coverage.tab --output out.vcf

Generate GC content file

The Generate_GC_tab.py script may used to generate gc content files: python Generate_GC_tab.py --fa reference.fa --size bin_size > gc_content.tab

note that AMYCNE requires the same bin size for the coverage

Generate coverage Files

Coverage tab files may be generated using TIDDIT. The files should be given in the following format:

#chromosome start end coverage quality

chr1 0 100 23 10

chr1 100 200 23 10

chr1 200 300 23 10

chr2 0 100 23 10

chr2 100 200 23 10

chr2 200 300 23 10

chrX 0 100 23 10

chrY 0 100 23 10

The quality column is optional, the header is also optional, and is not read by the software. The bins need to cover the entire genome.