mpileup -- bases missing

[Robby]

Hello everyone,
I created with with samtools a mpileup file out of a bam file, but some bases at the beginning and the end are missing in the mpileup, although the bases are covered by a few reads in the bam file. To exclude a quality problem I set the following parameter: -q 0 -Q 0 -C 0 -B, but the bases are still not in the mpileup.

What could be the problem. Has somebody an idea?

many thanks
Robby

[Heisman]

Try including "-A" and see if that makes a difference.

[Robby]

Thanks a lot. That worked perfectly .