Downsample a bam file

SimpleDownSample.sh

#intro

#This shows how to downsample a bam without returning to fastq state of the file...
#pros: Fast
#cons: Might have alignment artifacts/info from the bigger subpool (like better indel alignments). Worse then completely stripping alignment info and aligning the reads again.

#how to use

#create a config and edit the downsample fractions as seen below and run the samples or just remove the leading part and create one yourselfs.
#parallelisation is done in a lazy way and shoud be fixed/checked.
#p values should be doubled in case of paired reads from multiqc report.

cat << EOF > config.sh
i=/path/to/bam/sample.bam;p=0.69
i=/path/to/bam/sample2.bam;p=0.42
EOF
threads=3
set -ex

for line in $(cat config.sh) ; do 
	(
	export TMP_DIR="/scratch/$USER/projects/"
	mkdir -p $TMP_DIR
	. <(echo "$line")
	mkdir -p $(dirname $i)/../downsample/
	ml GATK/4.2.6.1-GCCcore-11.2.0-Java-11
	gatk --java-options "-Xmx4G -Djava.io.tmpdir=$TMP_DIR" RevertSam I=$i \
		REMOVE_DUPLICATE_INFORMATION=true \
		RESTORE_ORIGINAL_QUALITIES=false \
		REMOVE_ALIGNMENT_INFORMATION=false \
		RESTORE_HARDCLIPS=false \
		ATTRIBUTE_TO_CLEAR=null \
		O=$(dirname $i)/../downsample/$(basename $i .bam).revertsam.bam 
	gatk --java-options "-Xmx4G -Djava.io.tmpdir=$TMP_DIR" DownsampleSam \
		--INPUT $(dirname $i)/../downsample/$(basename $i .bam).revertsam.bam \
		--OUTPUT $(dirname $i)/../downsample/$(basename $i .bam).downsample.bam \
		--PROBABILITY $p \
		--METRICS_FILE $(dirname $i)/../downsample/$(basename $i .bam ).downsample.metrics.tsv
	gatk --java-options "-Xmx4G -Djava.io.tmpdir=$TMP_DIR" MarkDuplicates \
		--INPUT $(dirname $i)/../downsample/$(basename $i .bam).downsample.bam \
		--OUTPUT $(dirname $i)/../downsample/$(basename $i .bam).markduplicates.bam \
		--METRICS_FILE $(dirname $i)/../downsample/$(basename $i .bam).markduplicates.metrics.tsv
	gatk --java-options "-Xmx4G -Djava.io.tmpdir=$TMP_DIR" SortSam \
                --INPUT $(dirname $i)/../downsample/$(basename $i .bam).markduplicates.bam \
                --OUTPUT $(dirname $i)/../downsample/$(basename $i .bam).sorted.bam \
                --SORT_ORDER coordinate \
                --CREATE_INDEX true
	)&
	while [ $(jobs | wc -l ) -ge $threads ]; do echo "waiting"; jobs; sleep 30s ; done
done