I am new to creating bash scripts to run commands. I've tried to run this simple bash script to calculate the genome coverage of a bam file I have using the bedTools genomeCoverageBed command. I am not sure what I am doing wrong, but when I run this script I can a file that contains the printed command.
Here is my script:
echo "This is a Test:"
echo genomeCoverageBed -ibam $BAM_FILE -bg > WT_Rep_1_genomecov.bedgraph