BrAPI-Genotyping Concept Dictionary
Allele Matrix
The Allele Matrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier.
CallSet
A CallSet represents a Sample that was used during some sequencing event. In most cases, the CallSet will have a 1-to-1 relationship with a given Sample. However, in some cases, a single Sample may be used in multiple different sequencing events or experiments. The CallSet gives an identifier to the relationship between a Sample and a genotype sequencing event. In a VCF file, CallSets are the columns are the data matrix.
Call
From the GA4GH Variants specification: A Call encodes the genotype of an individual with respect to a variant, as determined by some analysis of experimental data.
Genome Maps
Notes on the GenomeMaps objects:
type: [Genetic | Physical]
unit: [cM | Mb]
linkageGroup: may be scaffold (i.e. linkageGroupCount may consist of chromosomes or scaffolds or a combination of the two)
For genetic maps, map naming convention should tell whether it is a consensus or mapping population (name of population) map for genetic maps
For physical maps, map naming convention should tell whether it is a reference genome (name of line) or pan-genome
Plates
API methods for tracking/managing Plates which contain Samples and related meta-data. A Plate is usually a plastic tray full of Samples, or a collection of test tubes grouped together.
Reference Sets
From GA4GH Variants schema documentation
A reference genome is a genome assembly that other genomes are compared to and described with respect to. For example, sequencing reads are mapped to and described with respect to a reference genome in the API, and genetic variations are described as edits to reference scaffolds/contigs. In the API a reference genome is described by a ReferenceSet. In turn a ReferenceSet is composed of a set of Reference objects, each which represents a scaffold or contig in the assembly. Reference sequences are expected to have unique names within a ReferenceSet
References
From GA4GH Variants schema documentation
A reference genome is a genome assembly that other genomes are compared to and described with respect to. For example, sequencing reads are mapped to and described with respect to a reference genome in the API, and genetic variations are described as edits to reference scaffolds/contigs. In the API a reference genome is described by a ReferenceSet. In turn a ReferenceSet is composed of a set of Reference objects, each which represents a scaffold or contig in the assembly. Reference sequences are expected to have unique names within a ReferenceSet
Samples
API methods for tracking/managing plant samples and related meta-data. A BrAPI Sample is the set of identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc).
VariantSets
Variants
A Variant describes a site of interest in a genetic sequence. It is usually described in terms of being compared to a Reference.
A Variant may also describe a more traditional marker, which can be positioned on a GenomeMap.
Vendor Samples
This interface is specific to facilities that performs an external analysis, such as genotyping facilities. The interface should be implemented by that facility’s server. The breeding database is the client of this interface.
Note that to use these calls, you likely have to use the authentication call prior to connecting (see Authentication best practices).