612a9d7fa6c688800bedf54ef3f9052e6bf93bbf
max
  Wed Dec 11 02:53:13 2019 -0800
makedoc update for refs #24626

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 4cff0d1..bb73642 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33314,35 +33314,41 @@
 
     cat fb.ponAbe3.chainHg19Link.txt
     # 2690870339 bases of 3043444524 (88.415%) in intersection
 
     cat fb.ponAbe3.chainSynHg19Link.txt
     # 2675805099 bases of 3043444524 (87.920%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev \
 	-buildDir=`pwd` ponAbe3 hg19) > rbest.log 2>&1
     # real    76m24.498s
 
     cat fb.ponAbe3.chainRBest.Hg19.txt
     # 2641865423 bases of 3043444524 (86.805%) in intersection
 
 ##############################################################################
-# addition of HGMD-restricted subset, Max, Jan 29 2019
-cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2018-10-01/
-cat /hive/data/outside/hgmd/2018.4-hgmd-public_hg38.tsv | cut -f7 | sort -u > hgmdTranscripts.txt
-zcat process/hg19.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
+# addition of HGMD-restricted subset, Max, Jan 29 2019, updated Dec 10 2019
+cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2019-11-21/
+year=2019
+#cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | sort -u > hgmdTranscripts.txt
+# change in 2019: ignore the version numbers, otherwise only 1815 transcripts left, big update by HGMD in 2019
+# adding "." so NM_123 doesn't match NM_123123
+cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | cut -d. -f1 | sort -u | awk '{print $1"."}' > hgmdTranscripts.txt
+cat process/hg19.curated.gp | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqHgmd hgmd.curated.gp
+$ wc -l hgmd.curated.gp 
+7965 hgmd.curated.gp
 #############################################################################
 # genomenom mastermind track, Max, Feb 2019
 cd /hive/data/genomes/hg19/bed/mastermind/
 wget 'https://mastermind.genomenon.com/cvr/download?format=csv' -O - > mastermind.2018.11.26.csv.gz
 unzip mastermind.2018.11.26.csv.zip
 mv mastermind_cited_variants_reference-2018.11.26-csv/ 2018-11-26
 hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > chromAlias.tab
 python ~/kent/src/hg/makeDb/mastermind/mastermindToBed.py 2018-11-26/mastermind_cited_variants_reference-2018.11.26.csv
 bedSort mastermind.bed mastermind.bed
 bedToBigBed -type=bed9+ -as=~/kent/src/hg/makeDb/mastermind/mastermind.as -tab mastermind.bed /hive/data/genomes/hg19/chrom.sizes  mastermind.bb
 ln -s `pwd`/mastermind.bb /gbdb/hg19/bbi/mastermind.bb
 #############################################################################
 2019-04-08: import of UCSC GENCODE group processing of GENCODE V30lift37 (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions