d52cbc57618c1635024918518f864f9a5f79ca12
max
  Tue Dec 10 03:52:17 2019 -0800
updating HGMD to 2019 version, refs #24625

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index f229b37..4cff0d1 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -32561,35 +32561,37 @@
 # # this caused a load problem.  One instance in the entire file where tissues not combined, ugh
 chr21   45650008        45650009        rs56323213      5       ENSG00000160223.12      ICOSLG  -10840  -0.484  -       0       1       skinExposed,    -0.484, 7.064,  0.005,
 chr21   45650008        45650008        rs145424134     8       ENSG00000160223.12      ICOSLG  -10841  -0.070  -       0       1       esophagusMuscular,      -0.070, 5.106,  0.008,
 
 # 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)
 # got hgmd 2017 from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com
 # see also the file hg38/hgmd.txt
+year=2019
 cd /hive/data/genomes/hg19/bed/hgmd
-cat /hive/data/outside/hgmd/2017.4-hgmd-public.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$/splicing variant/' | sort -k1,1 -k2,2n > hgmd.bed
+cat /hive/data/outside/hgmd/$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
 /usr/local/apache/cgi-bin/hgBeacon -f hgmd temp.bed hgmd
 # Forgot, finally done June 26: updated GBIB as qateam
 scp /gbdb/hg19/bbi/hgmd.bb hgdownload:/usr/local/apache/gbib/prot/
 
 ###########################################################################
 2018-03-08: update UCSC GENCODE V19 to include protein id (for VAI)
 
 cd /hive/data/genomes/hg19/bed/gencodeV19/
 # move tables that need to be rebuilt
 mkdir -p prev/pre-proteinId