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

diff --git src/hg/makeDb/doc/hg38/hgmd.txt src/hg/makeDb/doc/hg38/hgmd.txt
index 25dc592..ebe3945 100644
--- src/hg/makeDb/doc/hg38/hgmd.txt
+++ src/hg/makeDb/doc/hg38/hgmd.txt
@@ -1,12 +1,13 @@
 # got hgmd 2017 from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com
 # update 2019 Max
 # update 2020 Max
+# update 2021 Max
 cd /hive/data/genomes/hg38/bed/hgmd
 year=2020
 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