What is the principle of samtools depth?
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4 months ago
zt10122 ▴ 20

I wan't to compute depth,and if read1 and read2 all cover a base labeled as one,What should I do?

bioinformation samtools depth • 226 views
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4 months ago
seidel 9.4k

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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