Part1e_sort.sh

#!/bin/bash 
#SBATCH --job-name=bam_sort
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 1
#SBATCH --mem=40G
#SBATCH --qos=general
#SBATCH --partition=general
#SBATCH --mail-user=
#SBATCH --mail-type=ALL
#SBATCH -o %x_%j.out
#SBATCH -e %x_%j.err

hostname
date

module load picard/2.9.2
export _JAVA_OPTIONS=-Djava.io.tmpdir=/scratch

# son
IN=../align_stepwise/son.bam
OUT=../align_stepwise/son.sort.bam
java -jar $PICARD SortSam \
        INPUT=$IN \
        OUTPUT=$OUT \
        SORT_ORDER=coordinate \
        CREATE_INDEX=True

# mom
IN=../align_stepwise/mom.bam
OUT=../align_stepwise/mom.sort.bam
java -jar $PICARD SortSam \
        INPUT=$IN \
        OUTPUT=$OUT \
        SORT_ORDER=coordinate \
        CREATE_INDEX=True

# dad
IN=../align_stepwise/dad.bam
OUT=../align_stepwise/dad.sort.bam
java -jar $PICARD SortSam \
        INPUT=$IN \
        OUTPUT=$OUT \
        SORT_ORDER=coordinate \
        CREATE_INDEX=True


date