samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]]
Options:
-a
Output all positions (including those with zero depth)
-a -a, -aa
Output absolutely all positions, including unused reference sequences
-b FILE
Compute depth at list of positions or regions in specified BED FILE. []
-f FILE
Use the BAM files specified in the FILE (a file of filenames, one file per line) []
-l INT
Ignore reads shorter than INT
-m, -d INT
Truncate reported depth at a maximum of INT reads. [8000]
-q INT
Only count reads with base quality greater than INT
-Q INT
Only count reads with mapping quality greater than INT
-r CHR:FROM-TO
Only report depth in specified region.