Scripts for hereditary variants analysis, can be run independently or:
- Path to bed file
- Path to original fastq files
- Path to project
usage: utils.py [-h] [--test] [--debug] [--verbose] [--ori_fastq ORI_FASTQ]
[--ori_bed ORI_BED] [--project_path PROJECT_PATH]
[--show_steps]
Pipeline for hereditary variant analysis 'heriline'
python3.5 utils.py -fq fastq_path -b bed_file -p project_path
optional arguments:
-h, --help show this help message and exit
--test, -t Run pipeline on test mode
--debug, -d Run pipeline on debug mode
--verbose, -v Run pipeline with verbosity
--ori_fastq ORI_FASTQ, -fq ORI_FASTQ
Set path to the original fastq directory for symlink
to project
--ori_bed ORI_BED, -b ORI_BED
Set path to the original bed/manifest file for symlink
to project
--project_path PROJECT_PATH, -p PROJECT_PATH
Set path to the project directory
--show_steps, -s Show steps of the pipeline