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
  • check that the number of exceptions listed in snp###Exceptions and snp###ExceptionDesc match
  • make sure that there are no exceptions in the snp###Exceptions that do not also exist in the snp###ExceptionDesc table
  • 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 the names of the snps. Make sure that they make sense (no extraneous ones, all lower case, etc). The checkHgFindSpec tool with the -checkTermRegex option will check that all of the names in the snp### table match the regular expression specified in trackDb. There is not an option to run it on a single table, so just run it on the whole database and look for output specific to the snp table. For instance:

 checkHgFindSpec -checkTermRegex hg19

• 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