[Samtools-help] pileup format using -vcf

[Sarah S. <sas...@uc...>]

Hello,

I know this might be a silly question because the answer is probably out
there but I certainly can't find it....Using the -vcf option to generate my
pilup file and varFilter afterwards I get an output that looks like this:

5_22443 2247    G       R       228     228     50      84
.$...,,.anaaa.aA,,aaa.,,,,,,..aAA,,.Aa.aa.....Aa,AA,a.,a.,.AA.,,AaA,.A,..,,,A,.,.,,,^:,
BBB_bb[bBabbBbZ$


Its not complete at the end, but it is the first part I'm confused about.  I
see I have the coordinate, the variant base, the consensus base, and then
four columns of what? One of them is likely the number of reads, phred
scaled consensus quality, phred scaled probability of difference from
reference base, and maximum mapping quality, I think? But which is which?

Cheers, Sarah