Octopus: Genotyping and Haplotyping in Diverse Experimental Designs.

Haplotype-based variant callers have become the de facto choice for genotyping from next-generation sequencing (NGS) as they are able to resolve read-mapper alignment errors and implicitly phase heterozygous variants. Here, I describe how the haplotype-based variant calling tool Octopus can be used for genotyping and haplotyping in several common experimental designs.