Phred quality score

[Elena]

Dear IGV Team,

I'm using IGV 2.3.6.
I'd like to know if IGV can compute the average Phred quality score for a mismatched base in a specific position.
I know that it is possible to shade the mismatched bases by quality, but I need to summarize the quality of the mismatched base to study putative SNPs.
Do You have any suggestion regarding how fixing parameters to identity true SNPs?

Best regards,
Elena

[Jim Robinson]

Hi Elena,

First I suggest you update, we are now at 2.3.68.  

WRT "true" SNPs,  IGV is not a snp caller, and even snp callers have false positives and false negatives.    The rule for determining if a location should be colored in the coverage track uses a phred-quality weighted ratio, so it is already using the average quality information.   In particular the rule is 

(sum of phred quality scores of mismatches)  /  (sum of all phred quality scores)  >  threshold

where threshold is 0.2 by default, changeable in preferences.   That's what it does, but again it is not a snp caller,  there are other tools such as GATK for that.

Jim

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[Elena]

phred-quality weighted ratio is taken into consideration as rule only if 'quality weight allele fraction'' in Preferences is selected, is it?
Otherwise the rule for determining if the bar in the coverage track should be colored is given only by mismatch frequency, is it right?

[Jim Robinson]

That's correct, but it should be checked by default. If its not checked
then its just the sum of mismatch bases / total bases.