# Workflow and requirements 

# Computing environment
	The scripts used in this analysis are adapted to run using the Sun Grid Engine job scheduler
	If you run the scripts locally or on an HPC system with another scheduler, you will have to adapt them
	The scripts further use globally installed software in the form of modules which you will require prior to your analysis
	The required softwares are:
	
	bcftools/1.10.2
	bwa-mem2/2.2.1
	fastQValidator
	fastqc/0.11.9 
	gatk/4.1.4.1
	gcc/11.2.0
	htslib/1.10.2
	multiqc/1.12
	picard/2.22.0
	R/3.6.2
	samtools/1.10
	trimmomatic/0.39
	vcftools/0.1.16

# R environment
	As another prerequirement you need to install several R packages which are needed in individual steps.
	The installation is detailed in the script 00_R_Dependencies.R

# Data structure
	Prior to this analysis you will need to download the (raw) data and locate them into a directory such as
 	~/mydirectory/inputdata
 

 

