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