SNP Track QA

If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq. In addition to the SNP-specific checks on this page, be sure to follow the new track checklist, too.

• look at mysql tables
  • If possible, compare to old SNP tables for this species. Look for big jumps in the number of different func types of SNPs as well as the number and type of exceptions.
  • check that func types in snp### table are documented in the html, both in the methods and in the check boxes. If there are new func types, make sure they are displayed correctly in the browser
  • check that the weights column in snp### are only 1,2 or 3
  • look at the exceptionDesc table: spot-check the counts, make sure the exception messages show up on hgc pages, make sure the descriptions make sense. Ideally, this table would be visible in the Table Browser when the track is selected, but it isn't right now. See Redmine #3606 for current status of this problem.

• check settings (hgTrackUi and clicking on individual snp)
  • make sure that all settings that you can select for are present in mysql tables and vice versa
  • make sure that methods mention all func types that you can select in trackUi
  • check that can turn different gene tracks on in the trackUi

• • look at featureBits/Coverage for main snp table as well as the dbCoding and the ortho table. Also check coverage of haplo chromosomes.
  • see how coverage compares to old snp track if possible. Also when open up the track, most snps should match to the same place (though some will change)

• • make sure appropriate entries in hgFindSpec (this is very important for snps since the table is so large). Check that entries in hgFindSpec work by searching for some snps.
  • make sure track "turns off" when viewing large regions (table too large to load for large regions)
  • look at large snp insertions/deletions and check that display correctly in hgTracks and hgTrackUi

• description
  • make sure external files mentioned at the end of the html page exist at ncbi

• default position - is it turned on by default?

• if this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)"

AT RELEASE BE SURE TO:

1. push tableDescriptions and hgFindSpec
2. edit trackDb.ra so that old snp track is hidden by default if needed
3. make announcement on genome announce
4. notify Mark D so he can update LS-SNP
5. notify Galt so he can default to most current snp track in genome graphs