question about QUAL INFO

[kkamii]

Hi,

I want to use VarDict (version 1.6) to detect variants and decide the best quality option for my data.

To do that, Firstly I used vardict with default options.
And then, I adjusted -q option to 0 and compared two output.

One of the the newly detected mutation in the second output has QUAL INFO = 23.1, which exceeds the default base quality setting (22.5).

I don't understand why this mutation not detected in default option.

I tried more test ( with -q 5, 10, 15, 20 ) and the base quality of mutation is
-q option 0 -> QUAL = 23.1
-q option 5 -> QUAL = 22.4
-q option 10 -> QUAL = 21.5
-q option 15 -> QUAL = 21.5
-q option 20 -> QUAL = 21.5

why the QUAL info is continuely changed and how is the QUAL INFO calculated ?

plz answer me.

thank you very much :)

[kkamii]

plus, I want to know how I can adjust -q option without QUAL INFO change.

[PolinaBevad]

Hello @kkamii,

Sorry for the late reply, I'm quite busy at the moment with another project!

So the -q option really operates in two steps: when we iterate over reads and collect information about the variant, bases that are less than this threshold will not be considered - we skip them. And the second step: when all the information is collected, we filter out variants where mean quality was less than threshold. As you can see the first step can affect the variant base quality if you change threshold as some of the bases will not be included in final calculation for mean value.

It is good to not decrease threshold too hard because otherwise you can get some extra Complex/MNV variants, so keep it around default threshold (I recommend not less than 20 for Illumina).