giraffe-parameter-search

Workflow for testing vg giraffe parameters

Experiment config file config.yaml
Main snakefile 'Snakefile'
Sub-snakefile for graphing 'make_graphs.smk'
Graphing util 'scatter.py'
Parameter search util 'parameter_search.py' Parameter search util config file parameter_search_config.tsv

Warning

Mapping quality associated statistics incorrect.

How To Use

1. Edit parameter_search_config.tsv to contain the parameters you want to generate values for, and what way you want to generate them. See parameter_search.py for more information.

2. Run:

   python3 parameter_search.py --count x
   

   This will create the hash_to_parameters file.

3. Specify the graphs you want to generate in config.yaml.

4. Run:

   (umask 002; snakemake --configfile config.yaml --config experiment=map_hifi_10k -j128 --rerun-incomplete --use-singularity --singularity-args "-B /private" --latency-wait 120 --executor slurm --keep-going)
   

   Replace map_hifi_10k with experiment of choice from config.

TODO

• Add capability for more types of graphs and statistics
• Add capability for more realness, tech, subset settings via adding more experiment options
• Add variant calling sub snakefile
• Add more documentation (dedicated wiki)