On Mon, 17 Jun 2019, Karina Borlaug wrote:
I tried this command instead:
$samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -B -f Hg19.fasta sample.bam
But got the exact same output as without the -B option.
However as you point out it might be more valuable to keep the BAQ.
I am trying to extract the quality values with a python script in order to
create a frequency plot . I am still a little confused on why they are mixed
+33 and +64. Does it mean all of the ascii character in the output string is
BAQ scores and only some of them was converted to +64?
output string :
b>^=_=@=??]@A^AAbBBccBAcBBcB<LcBBBcBAA>BcBAABcBBcAb,AcCBC,CBBCddCBBBdCCCBcBBBACCBBC?cdBC!8A!c!C!CBBCBB?CC7CABA!aaAB@B!Bc!CCBC;CCABC!cCBAB!CB!BBd@B!?CB@ABC!A!CC!B`Bb!C!!!!!CCA?B<CC!BBCCCCCCCAC!CCAACA!A!!!!!!A!=!=A!
Or does it mean that only the +64 values are BAQ scores and the remaining +33
character are normal basequality values resulting in having to separate the two
different values when plotting a frequency plot.
I doubt that BAQ is the cause, as it should only reduce quality values and
never increase them. You might instead be seeing the result of the
overlap detection. This changes the quality values in read pairs where
the forward and reverse reads are long enough to overlap each other.
Where that happens, the lower-quality base in the pair will be set to zero
and the higher-quailty one to the sum of the two original quality values
if they agree, or to 0.8 x the highest if they disagree. To turn this
off, try the `-x` option:
samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -B -x -f Hg19.fasta sample.bam
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
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