Question: What is mean that mpileup read depth (read count) 0?
0
gravatar for Peavil
4 weeks ago by
Peavil10
Peavil10 wrote:

Hi,

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.

mpileup samtools • 155 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan62k • written 4 weeks ago by Peavil10
0
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan62k
Freiburg, Germany
Devon Ryan62k wrote:

There are no alignments there, that's all that it means.

ADD COMMENTlink written 4 weeks ago by Devon Ryan62k

thank you. I think I was mistaken for a while!

ADD REPLYlink written 4 weeks ago by Peavil10
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