convert_bams_to_fastqs.sh

#!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-01:00
#SBATCH -p short
#SBATCH --mem 4000
#SBATCH -o run_bam2fq_%A_%a.out
#SBATCH --array=0-17
#SBATCH --mail-user=alexander_gorelick@hms.harvard.edu  # Email to which notifications will be sent
#SBATCH --mail-type=ALL

## This pipeline should be run from FASTQ files to ensure that all preprocessing is standardized. 
## In case you only have access to BAM files and you aren't sure how they were generated, you can
## convert them back to FASTQs with this script.

module load picard/2.27.5
mkdir -p 00_fastq

## declare arrays
declare -a samples=("C157B1" "C157B2" "C157Di1" "C157Di2" "C157LN4" "C157N1" "C157P10" "C157P1" "C157P2" "C157P3" "C157P4" "C157P6" "C157P9" "C157TD1" "C157TD2a" "C157TD2b" "C157TD3" "C157TD7")

i=${SLURM_ARRAY_TASK_ID}
sample=${samples[$i]}

## convert the bam file back to PE-read FASTQs
BAM="original_bams/${sample}_aligned.bam"
FQ1="00_fastq/${sample}_R1_001.fastq"
FQ2="00_fastq/${sample}_R2_001.fastq"
java -jar $PICARD/picard.jar SamToFastq I=$BAM FASTQ=$FQ1 SECOND_END_FASTQ=$FQ2

## compress the fastq files
gzip $FQ1
gzip $FQ2