Haplotype Calling (beta)

This chapter describes the Genotype track and associated tools.

The Genotype track is a VCF inspired representation of alleles in database and sample genome context.

A suite of tools, so far including Microhaplotype Caller (beta), standard CLC variant track converter, VCF importer and exporter, is intended to serve as a framework to perform detailed haplotype-aware analysis of genomic variation.

This early version of tools for haplotype calling are intended solely for analysis of amplicon targeted panel data. Analysis of other types of data is not yet supported.

Note that the functionality of these tools is in beta. It is under active development and subject to change without notice. Generated results may not be accessible when later versions of the plugin are installed.


Complex region
A region with two or more overlapping loci.
'Countable' reads are sometimes also referred to as filtered reads. Which reads are 'countable' depends on the user settings when variant calling is performed - if e.g. the user has chosen 'Ignore broken pairs', reads belonging to broken pairs are not 'countable'.
A DNA fragment that gives rise to a single read or read pair. Note that, although overlapping paired reads have two reads in their overlap region, they are only counted as one when counting fragments in that region.
Variant Call Format. The file format specification can be found at GitHub https://samtools.github.io/hts-specs/ .