Small Indel Representation

All variants are reported in the VCF using symbolic alleles unless they are classified as a small indel, in which case full sequences are provided for the VCF REF and ALT allele fields. A variant is classified as a small indel if all of the following criteria are met:

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The variant can be entirely expressed as a combination of inserted and deleted sequences.

•

The deletion or insertion length is not 1000 or greater.

•

The variant breakends and/or the inserted sequence are not imprecise.

•

The variant has not been converted from a deletion to intra-chromosomal breakends by the depth-based SV classification routine.

When VCF records are output in the small indel format, they also include the CIGAR INFO tag describing the combined insertion and deletion event.