SNP Track QA

Starting with snp132, the SNP track was split into 4 tracks, announced here. Angie gave a presentation (video) on the big changes made starting with snp132. 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.

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 snp###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.

settings

• Make sure that there are no values in the snp### table that are not represented in the tracks filter controls. (see tip below)
  • Helpful: mysql> SELECT DISTINCT 'field' FROM 'snp###'; (repeat 4x where field is class, valid, func, molType)
  • Note that the controls in the cgi are hard coded, so you may find that controls exist for values not present in the snp### table.
• Try some table browser queries that use the checkboxes on the filter page.
• Try turning on selected gene tracks on track controls page, make sure results show up

 in the "UCSC's predicted function relative to selected gene tracks:" section.

• Try the various color options.

details

• Be sure to include a SNP with chimera and ls-snp links in your testing. To find such a SNP, pick any of the SNPs in the lsSnpPdb table (snpId column), go to that SNPs details page and then check the links under "Mappings to PDB protein structures".
• Make sure the tracks "turn off" when viewing large regions (these tables are too large to load for large regions).
• Pay special attention to the PAR regions and haplotype chromosomes. We shouldn't necessarily exclude snps that map to more than one position from sets that are uniquely mapped.

description

• Note that most of the description is the same on all 4 snp tracks -- this is kept in one file (snp132.shared.html for snp132) that is included in the other html with a line like:

 <!--#insert file="sharedText.html"-->

• Make sure the source files listed are correct and exist at NCBI.
• Make sure that "Interpreting and Configuring the Graphical Display" section mentions all func types that you can select in TrackUi.

snp###.fa files

These files will be located in /gbdb/$db/snp/. Be sure to request the push of these files from hgwdev to hgnfs1/genome-euro well in advance of the release. These files can be upwards of 33GB (and will likely keep growing!), and it can take 12 hours to transfer that much data from UCSC to genome-euro.

downloads

If this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)" (/usr/local/apache/htdocs-hgdownload/goldenPath/hg19/snp###Mask). 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]

genome graphs

You should not need to check with Galt about Genome Graphs using the most current version of the SNP track in Genome Graphs until at least snp145. Galt said that there is one place in chromGraphFactory.c where the snp### table just has to be listed to be found. This list currently goes all the way up to snp145. If you would like to check for yourself if the current snp### is this file you can run the following command in kent/src/hg/lib:

$ grep -in snp### chromGraphFactory.c

Using snp137 as an example:

$ grep -in snp137 chromGraphFactory.c 
217:"snp140", "snp139", "snp138", "snp137", "snp136",

If you find that your snp### track isn't listed, 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.