#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=24G
#SBATCH --time=10:00:00
#SBATCH --job-name=samtools_index
#SBATCH --mail-type=all
#SBATCH --mail-user=kah1g14@soton.ac.uk

# Index sorted .bam files

cd /mainfs/home/kah1g14/alignment/sorted/

module load samtools/1.16.1


for i in *_sorted.bam

do samtools index $i

done


for i in *_sorted.bam.bai

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

done