#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=24G
#SBATCH --time=08:00:00
#SBATCH --job-name=samtools_sort
#SBATCH --mail-type=all
#SBATCH --mail-user=kah1g14@soton.ac.uk

# Sort aligned /bam files

cd /mainfs/home/kah1g14/alignment/aligned_bam

module load samtools/1.16.1


for i in *_aligned.bam

do samtools sort $i > /mainfs/home/kah1g14/alignment/sorted/${i}_sorted.bam

done


# Remove '_aligned.bam' from sorted filenames

cd /mainfs/home/kah1g14/alignment/sorted


for i in *_aligned.bam_sorted.bam

do mv "$i" "${i/_aligned.bam/}"

done





