N+1 calling (or gVCF calling)

[shalabhsuman]

Is the tool optimized to perform variant calling (Exome or Whole Genome) on a large cohort of samples (>500) using N+1 method? Is it possible to have outputs in gVCF format?

[dancooke]

The "N + 1" problem is discussed in the wiki pages here. Calling of large cohorts has not been tested, and joint calling of sex chromosomes is currently under development (see this issue).

The current develop branch version supports reference calling (see this wiki page). Note however that Octopus does not report genotype likelihoods, so you will not be able to use GATK-style gVCF merging.

[simoncawley]

Hi Dan, I'm interested in trying out Octopus for calling reference, I was excited to see the link you posted above but sadly it leads to a blank page. Is there any documentation available in another location?