Samtools Depth Option For More Than One Bam Files

Hi everyone,

I’ve been stuck on this for several days. I want to use the samtools depth command but not only for a single bam file. I need to find a way to include all my bam files downloaded in the command.

Has anyone got an idea of how i can do this??

Thank you in advance,
Maria

The usage says that you can link multiple files, make sure the specify the options before the bam files

Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
   -b <bed>            list of positions or regions
   -f <list>           list of input BAM filenames, one per line [null]
   -l <int>            minQLen
   -q <int>            base quality threshold
   -Q <int>            mapping quality threshold
   -r <chr:from-to>    region