cover depth estimation with samtools depth and mpileup

Question

[Ирина]

Hello!

I am having a problem while estimating the depth of coverage in my data using samtools depth and samtools mpileup.

I got paired reads and performed sorting and indexing of the BAM files. However, when I use samtools depth and samtools mpileup to estimate the depth of coverage at specific coordinates, I get significant differences in the results. For example, the depth of coverage is 152520 for samtools depth and 19153 for mpileup. When checking reads in IGV, the depth matches the samtools depth results.

Could these more differences be due to overlapping reads? I can't understand why the mpileup results are significantly different.

Could you please suggest any ideas or approaches to investigate why the results are different?

Thank you in advance for your help.

[Pierre Lindenbaum]

Difference between samtools DEPTH and MPILEUP ; coverage per base using samtools depth and mpileup

Answer 1

[Huiyang]

Try PanDepth, a specialized tool for coverage and depth calculation that supports both short reads and long reads.