QUAL value from .vcf file is the phred score

Question

[cmatho]

Hello i am having some trouble interpreting .vcf files, I get values for QUAL that are really high (around 250) is this possible? For what I've read, this QUAL value is the phred score? And 10 to the (-QUAL/10) is the probability of that base calling to be wrong. Isn-t there a maximum for phred score that is 60? Thank you very much!!!!

Answer 1

[igor]

Depending on the variant caller, the QUAL score meaning can vary. For example, I've seen QUAL scores over 100,000.

[cmatho]

thank you very much, i have used vcf tools to creat the .vcf, would you say this is expected? Somehow I thought that this value was maximum 60 since the P would be extremely low for a QUAL value of 250!