Leveraging a Larger Family to detect DNMs
python3 Discover_DNMs.py -h
usage: Discover_DNMs.py [-h] [--depth_min DEPTH_MIN] [--depth_max DEPTH_MAX] [--input_file INPUT_FILE]
[--child [CHILD [CHILD ...]]] [--output_file OUTPUT_FILE] [--out_dir OUT_DIR] [--parent1_id PARENT1_ID]
[--parent2_id PARENT2_ID]
De Novo Mutations Discovery in the Offspring, Maher ALnajjar, 2025,
MATE-GBI-Genetics and Genomics Dep. Dr.Barta's LAB, Gödöllő, HUNGARY
optional arguments:
-h, --help show this help message and exit
--depth_min DEPTH_MIN, -d_min DEPTH_MIN
Define the MINIMUM Filtering Depth, default=15
--depth_max DEPTH_MAX, -d_max DEPTH_MAX
Define the MAXIMUM Filtering Depth, default=45
--input_file INPUT_FILE, -i INPUT_FILE
The file is a standard VCF file coming from GATK for example
--child [CHILD [CHILD ...]], -c [CHILD [CHILD ...]]
list of children sample id(s) separated by spaces, otherwise all samples in the vcf will be
considered
--output_file OUTPUT_FILE, -o OUTPUT_FILE
output file
--out_dir OUT_DIR, -o_dir OUT_DIR
indicate an output directory
--parent1_id PARENT1_ID, -p1 PARENT1_ID
One of the parents id
--parent2_id PARENT2_ID, -p2 PARENT2_ID
The other parent id