Variant Search Scope

From Array Suite Wiki

Jump to: navigation, search

In GeneticsLand, the search scope for views that list all known variants (e.g. the gene level All Snps table view) is a superset of the following Sources, which are indicated in the Source column. In other words, the user's Land data is supplemented with additional variants from dbSNP and other user-defined classifier data sources:


  1. Land - Variants with data in the Land including sample-level data (genotypes or allele doses) and association results
  2. dbSNP - Variants in dbSNP
  3. Others - Variants with evidence of existence based on reports from annotation sources (e.g. ExAC)
    • This set is defined in a file provided by OmicSoft which will be updated accordingly as annotation sources are updated.
      • The file is located at OmicsoftDirectory/Variant/NovelSnps/Human.B37.3_NovelSnps.sorted.gtt.gz
      • ArrayServer administrators may further supplement with additional known variants

Custom Novel Variants

To define additional variants, we create a VCF-like file with the first 5 columns sorted by CHROM and POS like this: Novel gtt.png

  • The ID is not used by the system so you may use a "." as the VCF missing value.
  • Add this file to the same OmicsoftDirectory/Variant/NovelSnps directory
  • Be sure to specify the genome (e.g. Human.B37.3) at the start of the name followed by an underscore.
  • The file must have the .gtt extension
  • You may add several files but performance is best with a single file.
  • You must restart ArrayServer for this new file to be recognized (a .bim index file will be generated at this time).
  • If you edit this file (e.g. to add new variants), you must delete the .bim file so it will be re-generated during ArrayServer start.