DP4 field & VCF parsing/SNP analysis

[idonaldson]

One answer was provided here:
http://www.biostars.org/p/67523/

"the mpileup -Q option, which by default is 13."

However, I am not sure this is completely correct as I have data with apparently good reads, but the total of DP4 is much less than DP.

Did you ever answer this question?

[jomaco]

Hi

In the samtools manual, for the DP4 field it states that the:

"...sum can be smaller than DP because low-quality bases are not counted."

I wonder, what is the cut-off for this? How low does the quality of a base need to be and what determines whether a base is low-quality?

Also, I've seen various tools described but my second question is this: in the parsing of VCF files to compare the specific depth at SNP positions shared between different samples are custom scripts usually used or does it largely depend on the application (as to whether the software is already available)?

I ask this as I am yet to see something specific to my needs but I also suppose it is quite a specific question. Is there a list or paper which you could direct me to which describes various SNP analysis programs and their applications? If this doesn't exist then I can try describe what I am trying to do but I think my main problem is simply not knowing what is out there.

Hope you can help

Thanks

Jon