Different coverage depth

Question

[wes]

I use the same bam file for both samtools mpileup (text pileup output) and weeSAM (visualization) analysis. However, I found out the coverage is not the same. For instance, weeSAM showed super high coverage,~116,000X, between region 10,045-10,084 due to AT repeats as shown in the image here but it is not detected in samtools mpileup. The same region only showed ~3,000X read coverage in samtools mpileup

1. Any idea why there is such differences?
2. How to adjust the setting in weeSAM in order to focus on those region with ~2000X coverage?

[Carlo Yague]

I don't know about weeSAM, but the depth of coverage in samtools mpileup is caped by the -d option (by default 250 but perhaps set to 3000 in your case):

  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [250]

[wes]

Thanks Carlo for answering my first question. I had rerun the samtools mpileup by increasing the depth coverage in the -d option. Hopefully, someone can answer my question as the current graph generated using weeSAM cannot give me a good view on the coverage of the other regions,