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For .vcf reporting - Do reference models change?

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  • For .vcf reporting - Do reference models change?

    To make a call on a variant as "derived" obviously means an "ancestral" value must be known so we know a change (mutation) has taken place.

    What are the reference models used in the .vcf files?

    Are they different by haplogroup? If so, will they be updated when the haplotree is updated?

    Will the reference models change over time? The reason I ask this is we may need to go back and re-download .vcf files if new vintages of reference models are used.

    What has triggered my questions is that in the latest wave of Big Y results I see a set of variants that appear broadly derived across several subclades. At the same, some of these do not appear as derived from the first wave of Big Y results. I did not go back and re-download the first wave .vcf files to see if those have changed.