cbffb0dd48c0c9621532fd6d129845128c743655
angie
  Fri Mar 13 11:04:18 2026 -0700
Made hg19ToHg38.chainBridge.over.chain.gz for MLQ #37156

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 0e5675d05e6..063dad39988 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -28975,30 +28975,58 @@
     # was modified to use the unmasked hg19/hg38 sequences
     doSameSpeciesLiftOver.pl -debug -stop=net -buildDir=`pwd` \
       -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev \
           -ooc=/hive/data/genomes/hg19/11.ooc hg19 hg38
     # Turns out the chain step procedure will not construct the proper
     # set of files in debug mode (pslParts.lst) because it can not.
     # the chain step has to be run for real:
     doSameSpeciesLiftOver.pl -continue=chain -buildDir=`pwd` \
       -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev \
           -ooc=/hive/data/genomes/hg19/11.ooc hg19 hg38 > chain.log 2>&1
 
     # verify the convert link on the browser is now active from hg19 to hg38
 
+##############################################################################
+# Bridge small double-sided gaps in hg38 liftOver chain (DONE 2026-03-13 - Angie)
+    cd /hive/data/genomes/hg19/bed/blat.hg38noMask.2013-12-31/run.chain
+    # Turn double-sided gaps in the all.chain into mismatches where appropriate:
+    chainBridge \
+        hg19.hg38.all.chain.gz \
+        /hive/data/genomes/hg19/hg19.2bit \
+        /hive/data/genomes/hg38/hg38.2bit \
+        stdout \
+    | pigz -p 8 > hg19.hg38.chainBridge.all.chain.gz
+
+    # Re-net the fixed all.chain:
+    chainNet \
+        hg19.hg38.chainBridge.all.chain.gz \
+        /hive/data/genomes/hg19/chrom.sizes \
+        /hive/data/genomes/hg38/chrom.sizes \
+        hg19.hg38.chainBridge.net /dev/null
+
+    # Extract the new & improved .over.chain from the new all.chain and net:
+    netChainSubset \
+        hg19.hg38.chainBridge.net \
+        hg19.hg38.chainBridge.all.chain.gz \
+        stdout \
+    | chainStitchId stdin stdout \
+    | pigz -p 8 \
+        > hg19ToHg38.chainBridge.over.chain.gz
+
+
 ##############################################################################
 # hg19 <-> hg38 difference tracks (DONE - 2013-12-28 - Hiram)
     # note: the procedure for this is in the hg38.txt file under
     # this same heading.  The end result is the loading of the table:
 
     cd /hive/data/genomes/hg19/bed/liftOverHg38
     hgLoadBed hg19 hg38ContigDiff hg19.itemRgb.bed
 
 
 ##########################################################################
 # NEANDERTAL AND DENISOVA METHYLATION (DONE 8/27/14 angie)
     # RM #13439
     mkdir /hive/data/genomes/hg19/bed/neandertalMethylation
     cd /hive/data/genomes/hg19/bed/neandertalMethylation
     wget http://carmelab.huji.ac.il/data/Reconstructed_Methylation_Neandertal.zip