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AF in vcf files

There is some inconsistency in the community on how to calculate the AF (allele frequency) value in vcf files. GATK calculates a hypothetical value (0, 0.5 or 1 for normal diploid organisms). Other callers will calculate the AF as an Alt Allele Frequency.

Is there a way to have both values in the VCF file from GATK?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think the AF in GATK VCFs are in concordance with the VCF spec. However, have a look at this thread for some other helpful information.


  • vangvang Member

    Hi Sheila
    I agree that that GATK VCF files are as described in the VCF specs. However, I need to be able to upload the VCF files to a diagnostic evaluation tool (in my case Cartagenia, https://www.agilent.com/en-us/promotions/cartagenia-overview). For filtering purposes in trio analyses, we need to remove variations below an allele frequency threshold. It is easy to calculate the frequency from the allele depths in the VCF file, but this is not currently possible within the software.

    It would be useful to have the values inside the VCF file. Is it possible to add this information to the vcf file using the JEXL expressions in your link?


  • vangvang Member

    Hi Sheila
    Ok, Thank you for your answer and explanation.


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