3f4772e689c620fa0db33a2522e362cdcc216047 braney Sat Oct 17 07:24:30 2020 -0700 almost done with the clinvar submissions track! diff --git src/hg/makeDb/doc/hg38/clinvarSubLolly.txt src/hg/makeDb/doc/hg38/clinvarSubLolly.txt new file mode 100644 index 0000000..32d7de1 --- /dev/null +++ src/hg/makeDb/doc/hg38/clinvarSubLolly.txt @@ -0,0 +1,23 @@ + +############################################################################# +# clinvarSubLolly track IN PROGRESS BRANEY 10/17/2020 +mkdir /cluster/data/hg38/bed/clinvarSubLolly +cd /cluster/data/hg38/bed/clinvarSubLolly +bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort -S 40g > sort.main.bed +hgsql hg38 -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):"$11}' tmp1 > tmp2 +paste tmp1 tmp2 > bigBedInput.bed + +bedToBigBed -as=$HOME/kent/src/hg/lib/clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/hg38/chrom.sizes clinvarSubLolly.bb +mkdir -p /gbdb/hg38/clinvarSubLolly +ln -s `pwd`/clinvarSubLolly.bb /gbdb/hg38/clinvarSubLolly/clinvarSubLolly.bb + +bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4,$13,$15,$18,$19}' | sort -S 40g > sort.main.bed +hgsql hg38 -Ne "select * from clinvarSub" | sort -S 40g > clinvarSubSub.txt +join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,0,"+",0,0,"0,0,0",$6,$20,$8, $9,$1,$10,$7,$11,$12,$13,$14,$15,$16,$17,$18,$19,$21}' | sort -S 40g -k1,1 -k2,2n | tawk -f assignScore > bigBedInput.bed + +bedToBigBed -as=clinvarSubBB.as -type=bed9+11 -tab bigBedInput.bed /cluster/data/hg38/chrom.sizes clinvarSub.bb +ln -s `pwd`/clinvarSub.bb /gbdb/hg38/clinvarSubLolly/clinvarSub.bb +