I finish preprocess a bam file like base recalibrator, mark duplicate, ... and then, I run samtools mpileup with the bam.
Most are in the form below.
chr1 1007432 g 30 .$,$.,,..AAa,.AAa,,AA.aAa.A..,a, 3>5>;::@]<>::==>>4E6>>=8876@6<
But, I could see rows that read depth is 0
chr6 32551911 C 0 chr6 32610535 A 0
How can I interpret read count is 0 data in mpileup result? (I already run IGV and, pick that position. As a result, there is no read)
Thanks for reading this story.