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PughLab pipeline-suite

This is a collection of pipelines to be used for NGS (both DNA and RNA) analyses, from alignment to variant calling.

Start by creating a clone of the repository:

cd /path/to/some/directory
git clone https://github.com/pughlab/pipeline-suite/

Additionally, the report generation portion of this tool requires installation of the BPG plotting package for R: https://CRAN.R-project.org/package=BoutrosLab.plotting.general

The pipeline-suite runs using parameters provided in YAML format. There are two types of required configuration files:

data configs:
- can be generated using create_fastq_yaml.pl; dna_fastq_config.yaml and rna_fastq_config.yaml
- bam_config.yaml, generated by any tool which outputs BAMs that are required for downstream steps
pipeline configs (dna_pipeline_config.yaml and rna_pipeline_config.yaml):
- these specify common parameters, including:
  - project name
  - sequencing type (wgs, exome, rna or targeted), sequencing center and platform
  - ref_type (ie, hg19 or hg38)
  - path to desired output directory (will be created if this is the initial run)
  - paths to tool-specific reference files/directories
  - desired versions of tools
  - and, for each tool, memory and run time parameters for each step

For tool-specific details for RNA-Seq configuration, click here: RNA-Seq.

For tool-specific details for DNA-Seq configuration, click here: DNA-Seq.