extract_fastq_from_bam.sh

#!/bin/bash

# Extracting paired fastq files directly from a BAM file
# https://gist.github.com/darencard/72ddd9e6c08aaff5ff64ca512a04a6dd
# This script requires a lot of disk space! (about 7 x BAM file size)
YSEQID="99999"
original_bam="${YSEQID}.bam"
threads=80

echo "Splitting BAM file..."
samtools view -b -f 1 -F 12 ${original_bam} > lib_002_map_map.bam &
# R1 unmapped, R2 mapped
samtools view -b -f 4 -F 264 ${original_bam} > lib_002_unmap_map.bam &
# R1 mapped, R2 unmapped
samtools view -b -f 8 -F 260 ${original_bam} > lib_002_map_unmap.bam &
# R1 & R2 unmapped
samtools view -b -f 12 -F 256 ${original_bam} > lib_002_unmap_unmap.bam &
wait

echo "Merging unmapped BAM files..."
# Merge the unmapped reads
samtools merge -@ ${threads} lib_002_unmapped.bam lib_002_unmap_map.bam lib_002_map_unmap.bam lib_002_unmap_unmap.bam
#rm -f lib_002_unmap_map.bam
#rm -f lib_002_map_unmap.bam
#rm -f lib_002_unmap_unmap.bam

# Sort BAM files by read name
echo "Sorting mapped BAM files by read name..."
samtools sort -@ ${threads} -n -o lib_002_mapped.sort.bam lib_002_map_map.bam 
echo "Sorting unmapped BAM files by Read name..."
samtools sort -@ ${threads} -n -o lib_002_unmapped.sort.bam lib_002_unmapped.bam 
#rm -f lib_002_map_map.bam
#rm -f lib_002_unmapped.bam

echo "Extracting fastq files from sorted BAM files..."
bamToFastq -i lib_002_mapped.sort.bam -fq lib_002_mapped.1.fastq -fq2 lib_002_mapped.2.fastq &
bamToFastq -i lib_002_unmapped.sort.bam -fq lib_002_unmapped.1.fastq -fq2 lib_002_unmapped.2.fastq &
wait
#rm -f lib_002_mapped.sort.bam
#rm -f lib_002_unmapped.sort.bam

echo "Merging and compressing of the paired end read fastq files..."
cat lib_002_mapped.1.fastq lib_002_unmapped.1.fastq | pigz - >> ../fastq/${YSEQID}_R1.fastq.gz &
cat lib_002_mapped.2.fastq lib_002_unmapped.2.fastq | pigz - >> ../fastq/${YSEQID}_R2.fastq.gz &
wait

echo "Conversion completed. Deleting unused files..."
#rm -f lib_002_mapped.1.fastq lib_002_unmapped.1.fastq lib_002_mapped.2.fastq lib_002_unmapped.2.fastq

echo "Done!"