e12aafdc608e1d74cc36b6707f54299910e8b7fe
max
  Tue May 28 02:30:36 2024 -0700
updating HGMD to 2023 version, refs #32001

diff --git src/hg/makeDb/doc/hg38/hgmd.txt src/hg/makeDb/doc/hg38/hgmd.txt
index 60df290..861ad3a 100644
--- src/hg/makeDb/doc/hg38/hgmd.txt
+++ src/hg/makeDb/doc/hg38/hgmd.txt
@@ -1,16 +1,18 @@
 # 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
+# update 2024 Max
 cd /hive/data/genomes/hg38/bed/hgmd
-year=2021
+year=2023
 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
 # wc -l says:
 # for 2021: 210260 hgmd.bed
+# 2023: 261922 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: the hg19/hg38 RefSeq HGMD subtracks
 # also update: hgmd on hg19, hgBeacon, the hgmd file for GBIB, see hg19.txt
 # for this, jump now to hg38/ncbiRefSeq.txt and hg19.txt