GATK's quality scores on VCF files
Posted in Ask the GATK team | Last updated on 2013-03-27 19:38:27


Comments (12)

Hi,

According to the link http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41.

quality score (phred score) is defined as below. (i.e. 1% error rate is equal to phred score of 20 (-10xlog 0.01))

QUAL phred-scaled quality score for the assertion made in ALT. i.e. -10log_10 prob(call in ALT is wrong). If ALT is ”.” (no variant) then this is -10log_10 p(variant), and if ALT is not ”.” this is -10log_10p(no variant). High QUAL scores indicate high confidence calls. Although traditionally people use integer phred scores, this field is permitted to be a floating point to enable higher resolution for low confidence calls if desired. If unknown, the missing value should be specified. (Numeric)

Using GATK to generate vcf files and looking through the quality column of those files, I found out that the max quality score is 441,453 which is extremely huge number.

I wonder if the quality score of GATK tool follows the phred score system; if not, how do you calculate the quality score and what do the numbers of quality score represent?

Look forward to hearing back from you soon and thank you very much.


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