Calculate Breadth of coverage from either a directory of bam and bai files, or from a single bam and bai file.
FOR THE CODIES OUT THERE:
git clone https://github.com/mattheww95/CrispyCody.git cd ./crispy_cody python3 setup.py install An environment.yml file is included in the directory to create a conda envrionment. This script requires pysam, so it will only run on linux (maybe mac too, but who the heck knows). Eventually crispy cody will get crispier, by adding in the ability to add the depth of a given postion to a provided VCF
The help output is provided below, if there any questions please e-mail me. Similarly if you are a Cody, just come ask me.
usage: crispy_cody.py [-h]
[-b BAM]
[-i BAM_INDEX]
[-t THRESHOLD]
[-d DIRECTORY_SCAN]
[-v VERBOSE]
[-l GENOME_LENGTH]
[-x LOG]
Calculate the breadth of coverage for a sequence
optional arguments: -h, --help show this help message and exit
-b BAM, --bam BAM Specify input bam file
-i BAM_INDEX, --bam_index BAM_INDEX Index file for bam to be calculated
-t THRESHOLD, --threshold THRESHOLD Set the threshold for the pileup coverage, default value is 5
-d DIRECTORY_SCAN, --directory_scan DIRECTORY_SCAN path to directory containing bams and bai files, files must have shared handle before first '.' appears
-v VERBOSE, --verbose VERBOSE Use a verbose output, default is False
-l GENOME_LENGTH, --genome_length GENOME_LENGTH Length of genome to be calculated, default is 29903
-x LOG, --log LOG Default is false, set to true to have output saved to log file in thecurrent working directory. Default is false, enter true for a log to be generated. A previous log file will be over written if present.The output location will be in the current directory