Create .bam file indexes for all bam files in a directory using samtools and parallel

indexBamFiles.txt

## Write a bash script for looping through the bam files


#! /bin/bash
for i in *accepted_hits.bam
do
	samtools index ${i}
done

## Save this files as indexBamFiles.sh

## To run in parallel (with 4 cores) 
ls *.bam | parallel -j4 -k bash indexBamFiles.sh {}