e5f2b5cb689c5bd5c71872a400884d70cd4d2413
markd
  Tue Mar 29 13:05:59 2022 -0700
Added liftover chains for T2T CHM13.  Clicking on these currently fails due to chromAlias issues.

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 4d1954e..db50aa3 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34749,15 +34749,51 @@
 cd panelApp
 ln -s /hive/data/genomes/hg19/bed/panelApp/genesPanel.bb
 ln -s /hive/data/genomes/hg19/bed/panelApp/STRsPanel.bb
 cd ~/kent/src/hg/makeDb/trackDb/human/hg19
 wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg19/panelapp.html
 cd ~/kent/src/hg/makeDb/trackDb
 mv human/hg19/panelapp.html human/hg19/panelApp.html
 curl https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg19/trackDb.txt >> trackDb.ra
 vi trackDb.ra
 make alpha DBS=hg19
 
 ###############################################
 
 #Probe and Microarray data sets addition 3/11/21
 
+#############################################################################
+# chm13 liftover alignments  (2022-03-29 markd)
+
+# preliminary CHM13 <-> hg19 liftOver chains until NCBI produces consensus alignments
+# provide by Nae-Chyun Chen <naechyun.chen@gmail.com>
+
+    mkdir -p /hive/data/genomes/hg19/bed/chm13LiftOver
+    cd /hive/data/genomes/hg19/bed/chm13LiftOver
+
+# Obtain GRCh37 from T2T Globus: team-liftover/v1_nflo/grch37-chm13v2.chain
+
+# rename to better match UCSC convetions and compress
+    mv grch37-chm13v2.chain hg19-chm13v2.over.chain
+    pigz hg19-chm13v2.over.chain
+
+# build bigChain files:
+    hgLoadChain -noBin -test none bigChain hg19-chm13v2.over.chain.gz 
+    sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab
+    bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../../chrom.sizes hg19-chm13v2.over.chain.bb
+    tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab
+    bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab  ../../chrom.sizes hg19-chm13v2.over.link.bb
+
+# link to gbdb
+  mkdir -p /gbdb/hg19/bbi/chm13LiftOver
+  ln -sf $(pwd)/*.bb /gbdb/hg19/bbi/chm13LiftOver/
+
+# make downloads, can't add to liftOver directory due to license in that directory
+  mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
+  ln -sf $(pwd)/hg19-chm13v2.over.chain.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
+  
+# push these files
+  /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.chain.bb
+  /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.link.bb
+  /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/hg19-chm13v2.over.chain.gz
+
+# NOTES: chromAlias doesn't work on click through yet, so disable for now