Hi,
I am trying the new version samtools 1.0. When I tried to use mpileup to
look for some positions, I noticed some strange base quality scores. For
example:
When I do
samtools mpileup -B -f h37_hg19.fa -r chr22:17538719-17538719 -q 0 -Q 0
test.bam
I get
[mpileup] 1 samples in 1 input files
<mpileup> Set
max per-file depth to 8000
chr22 17538719 T 13
<>,.,...,,.,, JIFbF=aIE!I!H
Removing -B gives the same results. These quality scores are not the
original base quality scores in the bam file. Also, "!" (phred+33), "a" and
"b" (phred+64) all appear. The original sequence is Phred+33. Does
samtools mpileup still make some changes to the base quality, even though I
specific -B (or --no-BAQ)? Is there a way to turn off this option?
Thanks,
BJ
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