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Different coverage depth

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 enter image description here

  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?
alignment
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written by wes • wes

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]
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written by Carlo Yague Carlo Yague

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,

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written by wes • wes

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