What is the principle of samtools depth?

Question

[Tao]

I want to compute depth, and if read1 and read2 all cover a base labeled as one. What should I do?

Answer 1

[seidel]

You should read the documentation on samtools depth, and then query the read depth at your position of interest as follows:

samtools depth input.bam -r chr1:1000-1000
chr1    1000    166

In this example, the read depth at base 1000 is 166. This means that in this data set, 166 reads cross this position.