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

• updateTimes.csh

make sure have most recent version

• makedoc

located at src/hg/makeDb/doc/{build}.txt

make sure that exists in makedoc

• 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 tracks for this species. Look for radical jumps in rows or particular types of SNPs.

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).

• 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

• all details for one data point (click through everything)

• featureBits, featureBits gap, countPerChrom.csh, and checkCoverage.csh

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)

• index

click "show sizes" in PushQ

• runJoiner.csh

• checkOffend.csh

check to see if any items off end of chromosome for all tables

• performance

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

check that display looks good

positionalTblCheck - script that checks to see if the table is ordered for faster access

• description

check spelling and grammar

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

emails sanitized

• default position - is it turned on by default?

• table descriptions - view table schema

• release log and release log url

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