The main scripts used for performning a CNV calling on maize genome based on Read Depth and CNVnator can be found. Inside the folder Complementary, the secondary scripts that are required for the workflow to work correctly are stored.
The script Preprocessing.sh is the first script to be run, since it contains all the steps from the trimming of the fasta files, to the creation of the final BAMfile.
Secondly, the CNV calling is performed by two methods:
- Extracting the mean read depth of each gene and comparing it against the total read depth of all the genes
- Using the tool CNVnator
In order to produce a better and easiest way to interpret the results, the script Table.sh, creates a table with as many columns as genes are studied and as many rows as individuals. The genes that contain a duplication will be masked with a 1, deleted genes will contain a -1 and standard genes will contain a 0. The last row will be a sum of the number of indivuals that present structural variation (either duplication or deletion) for each gene studied.