Indel Regions

Sites that are "filled in" inside deletions have additional changes:

All deletions:

Sites inside any deletion are marked with the deletion filters, in addition to any filters that have already been applied to the site.
Sites inside deletions cannot have a genotype or alternate allele quality score higher than the corresponding value from the enclosing indel.

Heterozygous deletions:

Sites inside heterozygous deletions are altered to have haploid genotype entries (eg, "0" instead of "0/0", "1" instead of "1/1").
Heterozygous SNV calls inside heterozygous deletions are marked with the SiteConflict filter and their genotype is unchanged.

Homozygous deletions:

Homozygous reference and no-call sites inside homozygous deletions have genotype "."
Sites inside homozygous deletions that have a nonreference genotype are marked with a SiteConflict filter, and their genotype is unchanged.
Site and genotype quality are set to "."

The described modifications reflect the notion that the site confidence is bound within the enclosing indel confidence.

On occasion, the variant caller produces multiple overlapping indel calls that cannot be resolved into 2 haplotypes. If this case, all indels and sites in the region of the overlap are marked with the IndelConflict filter.