Search functionality for the OncoArray-500K SNP chip
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
|Priority:||major||Milestone:||Variant Search v1.5|
Reggie will add VCF files with genotype data for the OncoArray 500K SNP chip (#1353). We should implement search functionality for this data set.
This search will have to work a bit differently than the other variant searches since it is not possible to index 500K variants for each item. This is due to limitations in the Lucene engine (max number of documents) and also due to performance.
Instead, the initial idea is to have a two-step search procedure. The first step is to have fixed database with gene and annotation information for the 500K variants on the chip. This search will return a list of SNP ID values. The second database is only indexing SNP ID values for each item in a way that makes it possible to search for REF (0/0), HET (0/1) or ALT (1/1) genotypes.