Generating pEA/sumEA matrix for any ML algorithm
- git clone https://github.com/maryamsamiei/pEA_Matrix_Generation.git
- conda env create -f ./BigPipeline/environment.yml
- conda activate pyBigPipeline
Required arguments:
| Argument | Descripion |
|---|---|
| --VCF | Path to annotated VCF file |
| --samples | Path to two-column CSV file with sample IDs in the first column and patient labels (cases=1, controls=0) in the second column. There should be no header row in the csv |
| --savepath | Path for output files |
| --cores | number of cpus to use |
Optional arguments:
| Argument | Descripion |
|---|---|
| --maxaf | sets maximum allele frequency threshold for ML pipelines (default: 0.01) |
| --minaf | sets minimum allele frequency threshold for ML pipelines (default: 0) |
| --method | pEA or sumEA matrix calculation. (options: pEA, sumEA) |
| --chrX | Whether to include (1) or exclude (0) sex chromosomes in analysis (options: 1, 0 / default: 1 ) |