samtools depth -r

0

Hi,

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.

I tried

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!


WGS

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