What is the principle of samtools depth?
1 answer
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.
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