Chado Schema and Extensions

There are currently two ways to store your genotypic data in Chado v1.3 with this module providing a third, more efficient way. You can see a comparison of the various methods below which should make it clear why we’ve gone with the storage method we have.

Comparison of Methods

Method	Name	Custom Tables	Supports Meta-data	# Tables	Comments
1	ND Experiment	No	Yes	14	Not suitable beyond 3 million genotype calls.
2	Stock Genotype	No	No	10	A good alternative if you don’t want to use custom tables but have a lot of data. Similar efficiency to Method #2 but less support for meta-data.
3	Genotype Call	Yes	Yes	10	Most efficient; although it touches the same number of tables as Method #3 there are less records per genotype call

All three methods store Markers & Variants in the same way. For the purposes of this module, a variant is a location on the genome where variation has been detected and has a type of SNP, MNP, Indel, etc. A marker then indicates which method the genotype calls associated with it were determined by. For example, you may have a variant on Chromosome 1 at position 45678 that you detected variation through two different methods. Each method would be indicated as a marker and all the genotype calls detected by that method would be attached to the appropriate marker and not directly to the variant. This has been determined necessary since the level of trust and how you interpret any quality meta-data will depend on the method.

Our Method: Custom Genotype Call Table

Now, lets consider the same example as in Method 1 (one VCF line with three alleles and six samples):

# Records	Tables	Example	Explanation
2	feature	“LcChr1p555” and “LcChr1p555 GBS Marker”	One each for variant and marker where the variant may already exist.
2	featureloc	Chr1:554-555 for each.	Locate each of the variant and marker on the chromsome.
1	feature_relationship	“LcChr1p555 GBS Marker” is_marker_of “LcChr1p555”	Link the marker and variant.
6	genotype_call	All Foreign Keys with the exception of any quality information you want to store in the meta-data column	This links the marker, variant, allele call, stock and project all in one and stores any addition quality information in the meta-data column.

Total: 11 records per line in a VCF with only 6 stocks and 3 alleles per variant.

Notice how efficient this method is. This is because (1) most of the foreign key connections are taking place in a single table (genotype_call) and (2) there now only needs to be a single record in the genotype table for “AA” rather than one record per marker using the previous method. For further comparison, the same 100,000 line VCF file would now only take 1,100,000 records to store not including the records for your chromosomes, which already exist, those for your stocks, only 6 per file, and those for you alleles (genotype table), which likely already exist. Furthermore, storing meta-data doesn’t increase the number of records like it would in the first method.

Note

For more information about the two methods supported by core Chado, see the ND Genotypes documentation on schema.