On 16 Sep 2015, at 22:24, Brendan Kohrn <[email protected]> wrote:
> 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.
One of the changes introduced back in 0.1.19 is that mpileup applies the -Q
minimum-base-quality filter to mpileup output. The default filter level is 13;
if you use -Q0 you'll get the same output with 0.1.19 (and the current 1.2) as
with 0.1.18 and before.
When these low-quality bases are filtered out, the depth at position 149 is 0,
and the following columns are empty, as one might expect -- the depth is 0 and
there are no read bases to display. However in some other circumstances (with
multiple input files) empty columns in mpileup output are shown as "*", and it
possibly ought to be displaying these empty columns due to low-base-quality
filtering similarly.
So in summary: this (empty fields) is indeed supposed to be happening, but
those fields likely ought to be being displayed in a less confusing way.
Thanks for the report.
John
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