03a_variant_calling_bluecp3.sh

#!/bin/bash
##################################
# Alexandra Jansen van Rensburg
# alexjvr@gmail.com
# Last modified 23/10/2018 09:35
##################################

# Creates submission script for variant calling using mpileup
# using arrays on BlueCrystal p3

#run job in working directory
cd $PBS_O_WORKDIR

#Define variables
HOMEDIR="G3_Hesperia_comma"
REFGENOME="Hesperia_comma_Red_MESPA.fasta"
JOBNAME="HC"


#load your program if it is installed globally or the modules you used to install your program locally (compilers, etc) 
#Specify modules
module load apps/samtools-1.8

~/bristol-velocity/AJvR_VelocityPipeline/wrapper/03a_call_SNVs_bluecp3.sh -i ~/$HOMEDIR/mapped/ -r ~/$HOMEDIR/RefGenome/$REFGENOME -o ~/$HOMEDIR/03_variants -c c -v 1 -d 0 -s 20 -p 0.05 -module1 apps/samtools-1.8 -job $JOBNAME_full.mpup;