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| 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 | new track checklist]], too.
| | This page is no longer maintained. |
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| * look at mysql tables
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| ** check that the number of exceptions listed in snp###Exceptions and snp###ExceptionDesc match
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| ** make sure that there are no exceptions in the snp###Exceptions that do not also exist in the snp###ExceptionDesc table
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| ** 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.
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| ** 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
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| ** check that the weights column in snp### are only 1,2 or 3
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| ** 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:
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| checkHgFindSpec -checkTermRegex hg19
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| * check settings (hgTrackUi and clicking on individual snp)
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| ** make sure that all settings that you can select for are present in mysql tables and vice versa
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| ** make sure that methods mention all func types that you can select in trackUi
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| ** check that can turn different gene tracks on in the trackUi
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| ** look at featureBits/Coverage for main snp table as well as the dbCoding and the ortho table. Also check coverage of haplo chromosomes.
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| ** 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)
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| ** 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.
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| ** make sure track "turns off" when viewing large regions (table too large to load for large regions)
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| ** look at large snp insertions/deletions and check that display correctly in hgTracks and hgTrackUi
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| * description
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| ** make sure external files mentioned at the end of the html page exist at ncbi
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| * default position - is it turned on by default?
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| * if this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)"
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| ==AT RELEASE BE SURE TO:==
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| # push tableDescriptions and hgFindSpec
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| # edit trackDb.ra so that old snp track is hidden by default if needed
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| # make announcement on genome announce
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| # notify Mark D so he can update LS-SNP
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| # notify Galt so he can default to most current snp track in genome graphs
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| [[Category:Browser QA tracks]]
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