4adc5c603e035b607c14f9953f4196eeca3f93d1
max
  Fri Aug 18 03:46:19 2023 -0700
hgmd 2021 update, refs #14280

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 353d53e..ba346b1 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -32184,58 +32184,61 @@
 
 # refine generated trackDb.gtexEqtl.ra file and install in makeDb/trackDb/human/hg19
 
 ########
 # Load 44 per-tissue tracks: gtexEqtlTissue<tissueName>
 csh $bin/getxEqtlLoadTissues.csh UCSC_output >&! loadTissuesV2.log &
 
 #NOTE: V2 was a second release that followed immediately after first release (which was timed to coincide
 #  with Nature paper pub.  V2 revised schema (added ensembl gene ID, additional summary fields)
 # and color conventions.
 
 ###########################################################################
 # HGMD (updated 12/10/19 max)
 # HGMD (updated 01/25/18 max)
 # HGMD (updated 12/12/20 max)
+# HGMD (updated 08/18/23 max)
 # got hgmd from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com
 # see also the file hg38/hgmd.txt
+# Got it from Georgios.Stamoulis@qiagen.com
 year=2020
 cd /hive/data/genomes/hg19/bed/hgmd
 cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg19.tsv | grep -v \# | tawk '{if ($5=="I") {start=$4-1; end=$4+1; col="100,100,100"} else if ($5=="D") {start=$4-1; end=$4; col="170,170,170"} else {start=$4-1; end=$4; col="0,0,0"}; print "chr"$3,start,end,$2":"$1,0,".",start,end,col,$2,$1,$5}' | sed -e 's/M$/substitution/' | sed -e 's/I$/insertion (between the two basepairs, sequence not provided by HGMD)/' | sed -e 's/D$/deletion (endpoint not provided by HGMD)/' | sed -e 's/X$/insertion-deletion (endpoint not provided by HGMD)/' | sed -e 's/R$/regulatory variant/' | sed -e 's/S$/splicing variant/' | sort -k1,1 -k2,2n > hgmd.bed
 bedToBigBed hgmd.bed /hive/data/genomes/hg19/chrom.sizes hgmd.bb -type=bed9+ -as=hgmd.as -tab
 ln -s /hive/data/genomes/hg19/bed/hgmd/hgmd.bb /gbdb/hg19/bbi/hgmd.bb
 hgBbiDbLink hg19 hgmd /gbdb/hg19/bbi/hgmd.bb
 # Forgot, finally done Oct 24: also updated hgBeacon
 bigBedToBed /gbdb/hg19/bbi/hgmd.bb /tmp/temp.bed
 python2 /usr/local/apache/cgi-bin/hgBeacon -f hgmd /tmp/temp.bed hgmd
 # Forgot, finally done June 26: updated GBIB as qateam
-scp /gbdb/hg19/bbi/hgmd.bb hgdownload:/usr/local/apache/gbib/prot/
+scp /gbdb/hg19/bbi/hgmd.bb hgdownload:/usr/local/apache/htdocs/gbib/prot/
 # next restrict RefSeq down to HGMD subset
 
-# addition of HGMD-restricted subset, Max, Jan 29 2019, updated Dec 10 2019
-cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27/
-year=2019
+# addition of HGMD-restricted subset, Max, Jan 29 2019, updated Dec 10 2019, again Aug 2023
+cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2022-03-16/
 # change in 2019: ignore the version numbers, otherwise only 1815 transcripts left, big update by HGMD in 2019
 # adding "." so NM_123 doesn't match NM_123123
 cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | cut -d. -f1 | sort -u | awk '{print $1"."}' > hgmdTranscripts.txt
-cat process/hg19.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
+zcat process/hg19.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqHgmd hgmd.curated.gp
 $ wc -l hgmd.curated.gp
 7965 hgmd.curated.gp in 2019
 8971 hgmd.curated.gp in 2020
+10451 hgmd.curated.gp in 2021
 
 # now continue the process at ../hg38/hgmd.txt
+# or ideally make a shell script for all this...
 
 #############################################################################
 # LASTZ human/hg19 vs. pig/susScr11 - (DONE - 2018-04-02 - Hiram)
     mkdir /hive/data/genomes/hg19/bed/lastzSusScr11.2018-04-02
     cd /hive/data/genomes/hg19/bed/lastzSusScr11.2018-04-02
 
     printf '# human vs pig
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
 BLASTZ_O=400
 BLASTZ_E=30
 BLASTZ_M=254
 # default BLASTZ_Q score matrix:
 #       A     C     G     T
 # A    91  -114   -31  -123
 # C  -114   100  -125   -31