Haplotype Proposal

The set discovered candidate variants are used to assemble candidate haplotypes in an semi-exhaustive manner. Unlike other haplotype-based variant calling tools such as GATK HaplotypeCaller, Octopus does not require direct read evidence of a haplotype for it to be proposed. The main benifit of this approach is that transative physical read phasing can be exploited to cofidently call haplotypes longer than a single template length. The main downside is the additional runtimes complexity associated with exploring all 2^N possible haplotypes given N/2 candidate non-overlapping variants.

Growth

During the growth phase, novel alleles as appended to the branches of the haplotype tree.

Lagging

Backtracking