Calling with samtools mpileup calls fewer SNPs than expected.

Question

[kimgeng]

Hello, I'm master course student, and I'm embarrased that I'm very poor at controlling bam files and samtools

I tried to variant_calling with samtools mpileup, but as a result, I got a few SNPs (fewer SNPs than expected)

As you can see in the picture below, the region chr1:5838170~5838179 showed >=15 depth when I used the command "samtools depth -q30 -Q30"

However, they showed only 1 depth when I called variants with mpileup command.

I used same threshold (-q30 -Q30), but the results were very different.

I don't know what should I do to solve this problem.

Is anybody there to solve this problem?