be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/doc/hg38/clinvarSubLolly.txt src/hg/makeDb/doc/hg38/clinvarSubLolly.txt index 32d7de1..4054a20 100644 --- src/hg/makeDb/doc/hg38/clinvarSubLolly.txt +++ src/hg/makeDb/doc/hg38/clinvarSubLolly.txt @@ -1,23 +1,25 @@ ############################################################################# -# clinvarSubLolly track IN PROGRESS BRANEY 10/17/2020 +# clinvarSubLolly track DONE BRANEY 12/14/2020 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 +# add the line break after v409 +#tawk '{print $1":"$2 + 1"-"$3" <br>Variants (submissions):"$11}' tmp1 > tmp2 +tawk '{print $1":"$2 + 1"-"$3" Variants (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