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

diff --git src/hg/makeDb/doc/hg38/hgmd.txt src/hg/makeDb/doc/hg38/hgmd.txt
index 5aa00db..60c2e50 100644
--- src/hg/makeDb/doc/hg38/hgmd.txt
+++ src/hg/makeDb/doc/hg38/hgmd.txt
@@ -1,6 +1,11 @@
 # got hgmd 2017 from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com
+# update 2019 Max
 cd /hive/data/genomes/hg38/bed/hgmd
-cat /hive/data/outside/hgmd/2017.4-hgmd-public_hg38.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$/splicing variant/' | sort -k1,1 -k2,2n > hgmd.bed
+year=2019
+cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.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/hg38/chrom.sizes hgmd.bb -type=bed9+ -as=hgmd.as -tab 
 ln -s /hive/data/genomes/hg38/bed/hgmd/hgmd.bb /gbdb/hg38/bbi/hgmd.bb
 hgBbiDbLink hg38 hgmd /gbdb/hg38/bbi/hgmd.bb
+# also update: hgmd on hg19, hgBeacon, the hgmd file for GBIB
+# also update: hg19/hg38 ncbiRefSeqHgmd, see hg38/ncbiRefSeq.txt and hg19.txt
+