I am using samtools to compute depth at a specific region. Here is my code:
samtools depth 1.bam 2.bam 3.bam -b 1.bed
the bed file is like this:
#chrom start end 1 1000 2000
this command output depth at each locus which is not I want.
samtools depth 1.bam 2.bam 3.bam -r 1:1000-2000
which output same result.
I am really confused how can I output the average depth. There should be only 1 value for each bam file.
Thanks in advance!