30308acabd47a5ba91516d88ee303ef0e3853f55
markd
  Tue Jan 21 19:11:12 2020 -0800
load GENCODE V19 MT sequences to chrMT

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index d42d412..296e033 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33989,15 +33989,28 @@
     ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg19 33lift37 99 'Jan 2020'
 
     # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
     # to describe new release. [ONLY if it's going to be pushed]
 
     # edit human/hg19/trackDb.gencode.ra to add new .ra file include
     make DBS=hg19
 
     # edit  all.joiner to add ~/tmp/gencodeV33lift37.joiner
     # verify with:
     pushd /hive/data/genomes/hg19/bed/gencodeV33lift37
     make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # commit all
 ##############################################################################
+2020-01-21: manually update GENCODE V19 to include chrMT (markd)
+
+  cd /hive/data/genomes/hg19/bed/gencodeV19/chrMT
+  # convert chrM annotation in gff3 to chrMT
+  zcat ../data/release_19/gencode.v19.annotation.gff3.gz | tawk 'NR==1{print;next} $1=="chrM"{$1="chrMT"; print}' >chrMT.gff3
+  # comprensive and basic are the same on chrM and there are no pseudogenes, so this is
+  # easy
+  cat ../tables/wgEncodeGencodeCompV19.gp chrMT.gp >wgEncodeGencodeCompV19.gp
+  cat ../tables/wgEncodeGencodeBasicV19.gp chrMT.gp >wgEncodeGencodeBasicV19.gp
+  
+  hgLoadGenePred -genePredExt hg19  wgEncodeGencodeCompV19 wgEncodeGencodeCompV19.gp
+  hgLoadGenePred -genePredExt hg19  wgEncodeGencodeBasicV19 wgEncodeGencodeBasicV19.gp
+##############################################################################