Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Phred-scaled quality scores Follow


  • Avatar
    Mahmoud Al-Bassam

    Thank you for the explanation. Super grateful! 


    Comment actions Permalink
  • Avatar
    Roller, Eric

    If there is 50/50 chance that the variant is present, what should the QUAL be?

    I would expect -10log10(0.5) = ~3
    But if you are normalizing similar to how your PL values are normalized then this may end up being
    -10log10(0.5/0.5) = 0

    Which one does GATK report and can you confirm if this is compliant with the VCF spec:
    QUAL — quality: Phred-scaled quality score for the assertion made in ALT. i.e. −10log10 prob(call in ALT is wrong). If ALT is ‘.’ (no variant) then this is −10log10 prob(variant), and if ALT is not ‘.’ this is −10log10 prob(no variant). If unknown, the MISSING value must be specified. (Float)

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk