6a26ac2de8a47a3700f5ccc9ca24572e39690f4a
angie
  Mon Nov 8 08:16:54 2010 -0800
Work in progress for #559: split snp131 into 3 subtracks:Common: uniquely mapped SNPs found by HapMap and/or 1000 Genomes;
Misc: uniquely mapped SNPs;
Non-unique: SNPs that map to more than one genomic location.
Currently I'm only using the validation codes by-hapmap and
by-1000genomes to separate Common and Misc; however, I really
should add a filter on allele frequency because the dbSNP doc
implies that some by-hapmap SNPs only found a single allele,
which would mean they validated that it's not a common SNP.
We don't get allele freq data from dbSNP; would need to fetch
new db dump files etc.  It would be great to include allele
freq data in the SNPs track if we go to the trouble, and Jim
has suggested adding a clinically associated bit (although
that bit can be triggered by the most tangential of associations,
like region endpoints in OMIM).  Spot-checking other validation
codes, none of them seem reliable enough to use as a basis for
Common. E.g. cluster might be from earlier+later version of same
submitter's bulk submission.

diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index a3480e9..b15549b 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -11539,30 +11539,31 @@
 registerTrackHandler("fishClones", fishClonesMethods);
 registerTrackHandler("mapGenethon", genethonMethods);
 registerTrackHandler("stsMarker", stsMarkerMethods);
 registerTrackHandler("stsMap", stsMapMethods);
 registerTrackHandler("stsMapMouseNew", stsMapMouseMethods);
 registerTrackHandler("stsMapRat", stsMapRatMethods);
 registerTrackHandler("snpMap", snpMapMethods);
 registerTrackHandler("snp", snpMethods);
 registerTrackHandler("snp125", snp125Methods);
 registerTrackHandler("snp126", snp125Methods);
 registerTrackHandler("snp127", snp125Methods);
 registerTrackHandler("snp128", snp125Methods);
 registerTrackHandler("snp129", snp125Methods);
 registerTrackHandler("snp130", snp125Methods);
 registerTrackHandler("snp131", snp125Methods);
+registerTrackHandler("snp131Composite", snp125Methods);
 registerTrackHandler("snp131Clinical", snp125Methods);
 registerTrackHandler("snp131NonClinical", snp125Methods);
 registerTrackHandler("ld", ldMethods);
 registerTrackHandler("cnpSharp", cnpSharpMethods);
 registerTrackHandler("cnpSharp2", cnpSharp2Methods);
 registerTrackHandler("cnpIafrate", cnpIafrateMethods);
 registerTrackHandler("cnpIafrate2", cnpIafrate2Methods);
 registerTrackHandler("cnpSebat", cnpSebatMethods);
 registerTrackHandler("cnpSebat2", cnpSebat2Methods);
 registerTrackHandler("cnpFosmid", cnpFosmidMethods);
 registerTrackHandler("cnpRedon", cnpRedonMethods);
 registerTrackHandler("cnpLocke", cnpLockeMethods);
 registerTrackHandler("cnpTuzun", cnpTuzunMethods);
 registerTrackHandler("delConrad", delConradMethods);
 registerTrackHandler("delConrad2", delConrad2Methods);