Calling with samtools mpileup calls fewer SNPs than expected.
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?
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