[Samtools-help] Explanation of -Q flag in vcfutils.pl varFilter.pl?

[Ian D. <Ian...@ma...>]

Please can someone explain what the -Q flag in 'vcfutils.pl varFilter'.

The only definition i can find is:

Usage: vcfutils.pl varFilter [options]

Options: -Q INT minimum RMS mapping quality for SNPs [10]

Does it corresponds to a Phred score?
Does it refer to the quality of a particular consensus base call or the SNP quality its (whatever that means)?

I would like to be able to filter SNPs using the mpileup pipeline and it looks as the -Q option might help?

Is this the same as (similar to) the 'samtools.pl varFilter' step used with pileup?  E.g.:

samtools.pl varFilter raw.pileup | awk '$6>=20' > final.pileup

Many thanks!
Ian

PS i asked question in Biostars this morning if anyone wants the points.  But non-one has answered yet. [http://biostar.stackexchange.com/questions/8873/meaning-of-samtools-vcfutils-pl-varfilter-q]