#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=24G
#SBATCH --time=12:00:00
#SBATCH --job-name=samtools_bam
#SBATCH --mail-type=all
#SBATCH --mail-user=kah1g14@soton.ac.uk

# Convert aligned .sam files to .bam

cd /mainfs/home/kah1g14/alignment/aligned_sam 

module load samtools/1.16.1


for i in *_aligned.sam

do samtools view -S -b $i > /mainfs/home/kah1g14/alignment/aligned_bam/${i}.bam

done


# remove '.sam' from .bam filenames

cd /mainfs/home/kah1g14/alignment/aligned_bam


for i in *_aligned.sam.bam

do mv "$i" "${i/.sam/}"

done








