[Breaking change] Variant QC changes to support multiallelics

We’ve changed hl.variant_qc to support multiallelics. This involves breaking changes to the schema produced. For instance, AF and AC are now arrays that include the reference allele. The GQ and DP statistics are also now not generated at all if those fields don’t exist.

Click through to the docs above to see the full story!

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It would also be useful to include MAF (minor allele frequency) metric when generating the variant_qc stats. The Hail tutorials seem to assume the AF is actually the MAF when screening out low frequency variants. But there are rare variants that are the REF allele and these get left in after filtering for AF < 0.01 instead of MAF < 0.01.

MAF is hl.min(mt.variant_qc.AF)

well, that’s the rarest allele at least.

good idea to change the tutorial though