7355201a77e934e6e7f28242d4beb15d694e7c8d braney Sun Oct 11 13:21:05 2020 -0700 initial work on Clinvar Submissions track #26330 diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt index 70a0649..95522b0 100644 --- src/hg/makeDb/doc/hg19.txt +++ src/hg/makeDb/doc/hg19.txt @@ -33697,45 +33697,43 @@ $buildDir/$db.rna.fa \ $pre) # pslMismatchGapToBed: NM_001365372.1 gapIx 9 shifted right 74 bases, but next block size is only 38; report to NCBI # pslMismatchGapToBed: NM_001288811.1 gapIx 1 shifted left 6 bases, but previous block size is only 5; report to NCBI # real 0m21.265s bedToBigBed -type=bed9+ -tab -as=$HOME/kent/src/hg/lib/txAliDiff.as $pre.bed \ /hive/data/genomes/$db/chrom.sizes $pre.bb # pass1 - making usageList (180 chroms): 77 millis # pass2 - checking and writing primary data (27362 records, 20 fields): 234 millis ln -sf `pwd`/$pre.bb /gbdb/hg19/ncbiRefSeq/$pre.bb ############################################################################# -# clinvarSub track IN PROGRESS BRANEY 8/4/20 -mkdir /cluster/data/hg19/bed/clinvarSub -cd /cluster/data/hg19/bed/clinvarSub -bigBedToBed /gbdb/hg19/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2,$4}' | sort > sort.main.bed -hgsql hg19 -Ne "select varId,clinSign from clinvarSub" | sort -n > clinSign.txt - -join -t $'\t' sort.main.bed clinSign.txt | cut -f 2- | sort -k1,1 -k2,2n -k5,5 | tawk -f gawk | tawk -f fawk > tmp1 -tawk '{print $1":"$2 + 1"-"$3"<BR>Variants (submissions):"$11}' tmp1 > tmp2 +# clinvarSubLolly track IN PROGRESS BRANEY 10/11/2020 +mkdir /cluster/data/hg19/bed/clinvarSubLolly +cd /cluster/data/hg19/bed/clinvarSubLolly +bigBedToBed /gbdb/hg19/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$3,$4}' | sort -S 40g > sort.main.bed +hgsql hg19 -Ne "select varId,clinSign,scv from clinvarSub" | sort -S 40g > clinvarSubSub.txt + +join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,$6,$1, $7}' | sort -S 40g -k1,1 -k2,2n -k5,5 | tawk -f makeFranklin | tawk -f assignColors > tmp1 +tawk '{print $1":"$2 + 1"-"$3"āVariants (submissions):"$11}' tmp1 > tmp2 paste tmp1 tmp2 > bigBedInput.bed -#join -t $'\t' sort.main.bed clinSign.txt | uniq -c | sed 's/^ *//' | sed 's/ /\t/' | tawk '{print $3,$4,$5, $6, $7, $1}' | sort -k1,1 -k2,2n > sorted.bed -# fawk written by "hand" -#tawk -f fawk sorted.bed > bigBedInput.bed -bedToBigBed -as=clinsub.as -type=bed9+2 -tab bigBedInput.bed /cluster/data/hg19/chrom.sizes clinsub.bb -ln -s `pwd`/clinsub.bb /gbdb/hg19 +bedToBigBed -as=$HOME/kent/src/hg/lib/clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/hg19/chrom.sizes clinvarSubLolly.bb +mkdir -p /gbdb/hg19/clinvarSubLolly +ln -s `pwd`/clinvarSubLolly.bb /gbdb/hg19/clinvarSubLolly/clinvarSubLolly.bb ############################################################################# # Trios for Genome In a Bottle - DONE 08/04/2020 ChrisL # see ~/kent/src/hg/makeDb/giab/make.txt ############################################################################# # COVID GWAS from COVID-19 Host Genetics Initiative Sep 2020 Kate # see ~kent/src/hg/makeDb/doc/covid/covidHgiGwas.txt ############################################################################# # gnomAD PEXT scores # PEXT data: # The baselevel is the sum of the expression value for all transcripts touching that base # The annotation-level is the sum of the expression of transcripts on which a variant has a