Handling * alleles

[ACEnglish]

Truvari doesn't consider ALT=* alleles and filters them the same a reference monozygotic (ALT=.) variants.

In section 1.6.1 of the VCF v4.5 specification, we see inside the definition for ALT that the ‘*’ symbol (allele missing due to overlapping deletion). My understanding is '' represents an allele which cannot be present and therefore isn't a variant per-say but more of an annotation that a variant call isn't possible (i.e. a 'null' variant). As a hypothetical example, the below diploid alignment would create a '' allele.

Hap1 - ATA---ATA
Hap2 - ATACTCATA
REF  - ATACGCATA 

CHROM POS ID REF  ALT ... GT
chr   3   .  ACGC A   ... 1|0
chr   5   .  G    T,* ... 2|1

These *-alleles would create redundancies for counting the variant states (TP/FP/FN) as its state is always equal to its overlapping deletion's state.

It gets even more complicated if we consider the possibilities of the SNP at position 5 as a TP or FP. Had the caller not made that SNP, the asterisks allele wouldn't be present and therefore we wouldn't be counted as a TP/FP (depending on the deletion's state).

This complication also holds if the above example is the baseline VCF and the caller did not report the SNP (a FN). In this case the asterisks allele must become a FN regardless of if its overlapping deletion is TP or FN.