prep_ref.sge

#!/bin/bash

#prep_ref.sge
#sge submission script to prepare the reference for BWA and GATK
#M. Supple
#last modified 8 August 2016

#usage  
#qsub fastqc.sge </path/to/ref> <reference.fasta>

#requires 
#bwa
#picard-tools
#samtools

#output
#creates various dictionaries in indexes



#sge submission info
#$ -N prep_ref
#$ -o prep_ref.output
#$ -l virtual_free=20g,h_vmem=20.1g
#$ -cwd
#$ -j y



#print some sge info
echo Job $JOB_NAME started `date` in queue $QUEUE with id=$JOB_ID on `hostname`

#read in input
refpath=$1
reference=$2
file=${reference%.fa}
file=${file%.fasta}
echo $file


#create bwa index
if (test -e $refpath$reference.bwt)
        then echo "skipping bwa indexing...already exists"
        else echo "creating bwa index"
                bwa index $refpath$reference
fi


#create picard dictionary for GATK
if (test -e $refpath$file.dict)
	then echo "skipping picard dictionary...already exists"
	else echo "creating picard dictionary"
		java -jar /home/msupple/programs/picard-tools-2.5.0/picard.jar CreateSequenceDictionary \
			R=$refpath$reference \
			O=$refpath$file.dict
fi


#create samtools index
if (test -e $refpath$reference.fai)
        then echo "skipping samtools indexing...already exists"
        else echo "creating samtools index"
		samtools faidx $refpath$reference
fi


#print note that job completed
echo done `date`