humanomics

Pipelines for analyses of -omics experiments in human

Usage

For now, just run:

./0--ConfigurePipeline.bash
./0--MakePipeline.py -c <pipeline.conf>

This will start by writing a configuration file (pipeline.conf, by default) which will be used to produce the following SLURM scripts:

0--FastQC.bash
1--MappingAndPreProcessing.bash
2a--QualityControl.bash
2b--HaplotypeCaller.bash
3--GenotypingAndRecalibrating.bash