66d4db32ebb42c4b5005e6c39a733bc1b75457d0
max
  Mon Dec 8 08:06:52 2025 -0800
fixing clinvar bigbed type bug, refs #36810

diff --git src/hg/utils/otto/clinvar/clinVarToBed src/hg/utils/otto/clinvar/clinVarToBed
index afaba972c6d..0d4d1fa8790 100755
--- src/hg/utils/otto/clinvar/clinVarToBed
+++ src/hg/utils/otto/clinvar/clinVarToBed
@@ -1092,31 +1092,31 @@
     if len(parts) == 4: # clinvarMain.hg19.2011-11-11.bed
         base, db, date, ext = parts
     else:
         base, db, ext = parts
 
     base = basename(base)
         
     tmpFname = "%s.%s.temp.bb" % (base, db)
 
     asFname = "clinvar.as"
     extraOptions = "-extraIndex=_dbVarSsvId,snpId,vcvId,_vcvIdVersion "
     if "Decor" in fname:
         asFname = "clinvarDecoration.as"
         extraOptions = ""
 
-    cmd = "bedToBigBed %s -tab -type=bed9+ -as=%s %s /hive/data/genomes/%s/chrom.sizes %s" % (extraOptions, asFname, fname, db, tmpFname)
+    cmd = "bedToBigBed %s -tab -type=bed12+ -as=%s %s /hive/data/genomes/%s/chrom.sizes %s" % (extraOptions, asFname, fname, db, tmpFname)
     mustRun(cmd)
 
     finalFname = "%s/%s.%s.bb" % (bigBedDir, base, db)
     tableName = finalFname.split('.')[0] # e.g. clinvarMain
 
     tmpFnames.append( (db, tableName, tmpFname, finalFname) )
 
 # make it atomic by renaming the temp files to the final file names at the very end
 for db, tableName, tmpFname, finalFname in tmpFnames:
     logging.debug("Renaming %s to %s" % (tmpFname, finalFname))
     os.rename(tmpFname, finalFname)
 
 # create the version.txt file
 clinvarVersion = open(versionFname).read()
 versionString = "ClinVar Release: %s, converted at UCSC on %s" % (clinvarVersion, date.today().strftime("%Y-%m-%d"))