54197358a1407de6898c360a38df822257338112 max Tue Dec 15 05:33:49 2020 -0800 updating hgmd and ncbiRefseqHgmd to HGMD 2020, refs #24625 diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt index 6770282..316904c 100644 --- src/hg/makeDb/doc/hg19.txt +++ src/hg/makeDb/doc/hg19.txt @@ -32138,43 +32138,59 @@ 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 $bin/getxEqtlLoadTissues.csh UCSC_output >&! loadTissuesV2.log & #NOTE: V2 was a second release that followed immediately after first release (which was timed to coincide # with Nature paper pub. V2 revised schema (added ensembl gene ID, additional summary fields) # and color conventions. ########################################################################### # HGMD (updated 12/10/19 max) # HGMD (updated 01/25/18 max) -# got hgmd 2017 from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com +# HGMD (updated 12/12/20 max) +# got hgmd from Frank Schacherer Frank.Schacherer@qiagen.com and Rupert Yip Rupert.Yip@qiagen.com # see also the file hg38/hgmd.txt -year=2019 +year=2020 cd /hive/data/genomes/hg19/bed/hgmd cat /hive/data/outside/hgmd/$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$/splicing variant/' | sort -k1,1 -k2,2n > hgmd.bed bedToBigBed hgmd.bed /hive/data/genomes/hg19/chrom.sizes hgmd.bb -type=bed9+ -as=hgmd.as -tab ln -s /hive/data/genomes/hg19/bed/hgmd/hgmd.bb /gbdb/hg19/bbi/hgmd.bb hgBbiDbLink hg19 hgmd /gbdb/hg19/bbi/hgmd.bb # Forgot, finally done Oct 24: also updated hgBeacon bigBedToBed /gbdb/hg19/bbi/hgmd.bb /tmp/temp.bed -/usr/local/apache/cgi-bin/hgBeacon -f hgmd temp.bed hgmd +python2 /usr/local/apache/cgi-bin/hgBeacon -f hgmd /tmp/temp.bed hgmd # Forgot, finally done June 26: updated GBIB as qateam scp /gbdb/hg19/bbi/hgmd.bb hgdownload:/usr/local/apache/gbib/prot/ +# next restrict RefSeq down to HGMD subset + +# addition of HGMD-restricted subset, Max, Jan 29 2019, updated Dec 10 2019 +cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27/ +year=2019 +# change in 2019: ignore the version numbers, otherwise only 1815 transcripts left, big update by HGMD in 2019 +# adding "." so NM_123 doesn't match NM_123123 +cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | cut -d. -f1 | sort -u | awk '{print $1"."}' > hgmdTranscripts.txt +cat process/hg19.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp +hgLoadGenePred -genePredExt hg19 ncbiRefSeqHgmd hgmd.curated.gp +$ wc -l hgmd.curated.gp +7965 hgmd.curated.gp in 2019 +8971 hgmd.curated.gp in 2020 + +# now continue the process at ../hg38/hgmd.txt ############################################################################# # LASTZ human/hg19 vs. pig/susScr11 - (DONE - 2018-04-02 - Hiram) mkdir /hive/data/genomes/hg19/bed/lastzSusScr11.2018-04-02 cd /hive/data/genomes/hg19/bed/lastzSusScr11.2018-04-02 printf '# human vs pig BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_O=400 BLASTZ_E=30 BLASTZ_M=254 # default BLASTZ_Q score matrix: # A C G T # A 91 -114 -31 -123 # C -114 100 -125 -31 @@ -32776,42 +32792,30 @@ # real 62m32.858s 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, 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 ############################################################################## # DGV GOLD (DATABASE OF GENOMIC VARIANTS GOLD STANDARD) (DONE 5/06/19 ChrisL) # Redmine #23371 ##############################################################################