[Samtools-help] query about mpileup and bcftool calls

[Prasun Dutta]

Hello,

I was calling variants from RNAseq data using samtools mpileup|bcftools
call. I am aware that the BAQ (base alignment quality) strategy is invoked
by default in mpileup. BAQ is in itself derived from the original base
quality score. Now if the BAQ is lower, no variants will be called in that
base. What is the general range of BAQ? How much is high and how much is
low? Is the BAQ score reflected in the VCF file in any form?

I was also wondering for a way visualize an mpileup file? What can be the
best way to do it?