I found the following issue in the output from samtools mpileup (-f), with
a single bam file input:
gi|255961284|ref|NC_011713.2| 140 G 1 ,$ C
gi|255961284|ref|NC_011713.2| 149 A 0
gi|255961284|ref|NC_011713.2| 150 C 1 , D
gi|255961284|ref|NC_011713.2| 151 G 1 , D
This has happened at locations with 0 depth in a few other files. This
issue doesn't appear to occur in samtools v. 0.1.17, but it does occur in
0.1.19 and up. I'm not sure about 0.1.18.
My question is: is this supposed to be happening, or is it (as I think it
is) a bug?
Brendan Kohrn
Cruzan Lab
Portland State University
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