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
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
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