ReduceReads.qsub

#!/bin/bash
filename=$1
#filename=$(basename "$fullfilename")
extension="${filename##*.}"
export filebase="${filename%.*}"

if [[ $extension -ne "bam" ]]; then
    echo "BAM input only"
    exit
fi

export picard=/ifs/home/c2b2/rr_lab/shares/picard-tools-1.84
export gatk=/ifs/home/c2b2/rr_lab/shares/GenomeAnalysisTK-2.3-6-gebbba25
export bundle=/ifs/scratch/c2b2/rr_lab/shares/ftp.broadinstitute.org/bundle/2.3

#############################################
## REDUCEREADS WITH GATK
#############################################

qsub_output=$( cat << 'EOF' | qsub
#$ -l mem=7G,time=1::
##$ -m ae
#$ -N ReduceReads
#$ -t 1-25
#$ -V

java -Xmx6G -jar $gatk/GenomeAnalysisTK.jar \
    -T ReduceReads \
    -I $filebase.bam \
    -R $bundle/hg19/ucsc.hg19.fasta \
    -L chr$(chr $SGE_TASK_ID) \
    -o $filebase.reduced.chr$(chr $SGE_TASK_ID).bam 
EOF
)
echo $qsub_output
jid=$(echo $qsub_output | cut -d" " -f3 | cut -d. -f1)

#############################################
## MERGE WITH PICARD
#############################################
qsub_output=$( cat << 'EOF' | qsub -hold_jid $jid
#$ -pe smp 2
#$ -l mem=2G,time=2::
#$ -N ReduceReads_merge
#$ -m ae
#$ -V

java -Xmx2G \
-jar $picard/MergeSamFiles.jar \
OUTPUT=$filebase.reduced.bam \
ASSUME_SORTED=true \
USE_THREADING=true \
INPUT=$filebase.reduced.chr1.bam \
INPUT=$filebase.reduced.chr2.bam \
INPUT=$filebase.reduced.chr3.bam \
INPUT=$filebase.reduced.chr4.bam \
INPUT=$filebase.reduced.chr5.bam \
INPUT=$filebase.reduced.chr6.bam \
INPUT=$filebase.reduced.chr7.bam \
INPUT=$filebase.reduced.chr8.bam \
INPUT=$filebase.reduced.chr9.bam \
INPUT=$filebase.reduced.chr10.bam \
INPUT=$filebase.reduced.chr11.bam \
INPUT=$filebase.reduced.chr12.bam \
INPUT=$filebase.reduced.chr13.bam \
INPUT=$filebase.reduced.chr14.bam \
INPUT=$filebase.reduced.chr15.bam \
INPUT=$filebase.reduced.chr16.bam \
INPUT=$filebase.reduced.chr17.bam \
INPUT=$filebase.reduced.chr18.bam \
INPUT=$filebase.reduced.chr19.bam \
INPUT=$filebase.reduced.chr20.bam \
INPUT=$filebase.reduced.chr21.bam \
INPUT=$filebase.reduced.chr22.bam \
INPUT=$filebase.reduced.chrX.bam \
INPUT=$filebase.reduced.chrY.bam \
INPUT=$filebase.reduced.chrM.bam

samtools index $filebase.reduced.bam
rm -rf $filebase.reduced.chr*.bam*
EOF
)
echo $qsub_output
jid=$(echo $qsub_output | cut -d" " -f3 | cut -d. -f1)

export jid