samtools mpileup not filtering reads that fail mapping/base quality filters

[tracecakes]

Hi all,

I was wondering if anyone could help me with this issue. I am trying to create VCF files using samtools mpileup and would like to filter out reads based on mapping/base quality scores. So I use the -q and -Q options:

samtools mpileup -C 50 -Q 20 -q 20 -r38:92029-92031 -SDuf canfam3.fasta 561_final.bam | bcftools view -cg -

And get this as output:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Puli_516
38 92030 . C T 33.5 . DP=9;VDB=0.0099;AF1=1;AC1=2;DP4=1,3,1,3;MQ=20;FQ=-29;PV4=1,0.00038,1,1 GT:PLP:SP:GQ 1/1:63,2,0:8:0:5

In the VCF specification it says that DP4 and DP in the format column only include "high quality" bases and reads - however the output does not reflect this because if I look at this site in tview there are many poor quality bases/reads (see attached image). I would expect something like DP4=0,0,1,3 and DP=4 in the format column. This happens at pretty much every site.

If anyone could give me any ideas about what is happening it would be a big help.

Thanks!