SNP Track QA

Starting with snp132, the SNP track was split into 4 tracks, announced here. 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 section of the description page mentions 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 the source files listed are correct and exist at ncbi

• downloads - If this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)" Check hat the FASTA files are actually masked with snps. Look for some lines with y, w, m, etc. Can use a command like:

  zcat chr1.subst.fa.gz | head -300 | grep -i [^atgcn]

• be sure to include a snp with chimera and ls-snp links in your testing. To find such a SNP, look in the lsSnpPdb, and then check the links under "Mappings to PDB protein structures" on the track details page.

• check with Galt to make sure that the current snp track will be used in genome graphs. (rsID is one of the accepted genome graphs formats. When rsIDs are entered, their positions are looked up in the snp table. Galt said in April 2011 that currently: "It starts looking for snp134, then snp133, ... down to about snp125. The first one it finds that exists in the db is returned and used for resolving user symbols that might be rsIds."

AT RELEASE BE SURE TO:

• make the old SNP track (if any) hidden by default, and check to see if any old SNP tracks should be dropped from the RR.
• announce the release on genome-announce.
• when you push the snp-masked downloads, add a link to downloads.html.