alleleSelector

From a genome alignment, this program finds possible candidate windows for variant calling.

Dependencies

python3.5+, pysam

Example run:

python3 main.py --bam [path_to_bam] --ref [path_to_reference_fasta_file] --chromosome_name chr3 --max_threads [max_number_of_threads] --test [True/False] --json [True/False]