704efd7a1be11b0d69aff4a9101f87ed5b62734d
angie
  Thu Jan 23 10:10:10 2020 -0800
Add NC_012920 (rCRS) mitochondrion to hg19 as chrMT.  refs #24648

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 296e033..b64bdcc 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -30778,30 +30778,34 @@
 cd ..
 
 # redo trackDb
 
 hgGtexExonBed hg19 -trackDb -bright gtex ../gencode/gencode.v18.genes.patched_contigs_exons.txt
 
 #############################################################################
 # GTEx V6 (October 2015) Kate
 # Create BED from hgFixed tables (see doc/gtex)
 # Reload with scores (see hg38/gtex.txt)
 
 cd /hive/data/outside/gtex/V6
 
 # Load gene models (Gencode V19 transcript union from GTEx)
 gunzip gencode.v19.genes.patched_contigs.gtf.gz
+
+# NOTE FOR NEXT TIME: hg19 now has chrMT, so leave "chrMT" as-is instead of changing to chrM.
+# optional: liftOver from chrMT (NC_012920) coords to chrM (NC_001807).
+
 awk '$1 !~ /^#/ {print "chr"$0}' gencode.v19.genes.patched_contigs.gtf | sed 's/chrMT/chrM/' | \
         gtfToGenePred stdin gencodeV19.hg19.genePred
 hgLoadGenePred hg19 gtexGeneModelV6 gencodeV19.hg19.genePred -infoOut=gtexGeneModelInfoV6.tab
 
 # Get transcript for each gene
 A#tail -n +2 gtexGeneModelInfoV6.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV6.tab
 #hgLoadSqlTab hgFixed gtexTranscriptV6 ~/kent/src/hg/lib/gtexTranscript.sql gtexGeneTranscriptsV6.tab
 
 # Load BED table
 cd /hive/data/genomes/hg19/bed
 mkdir -p gtex
 cd gtex
 
 set gencode = V24lift37
 # use latest attribute annotaion