73beb2ce1a8cef6d6e33fb28f95d5871c89d47f1
braney
  Wed Aug 5 15:50:31 2020 -0700
starting work on clinsub track

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 31f53ef..34ad16c 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33667,16 +33667,25 @@
 642.857786 ********************************* 248
 714.286429 *************************** 80
 785.715071 ************** 10
 857.143714 ******** 4
 928.572357 *************** 12
 
 # table looks OK, load it
 set lib = ~/kent/src/hg/lib
 hgLoadBed hg19 -noBin -tab -type=bed6+4 \
         -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \
                 gtexGeneV8 gtexGeneBedV8.bed
 # Read 54481 elements of size 10 from gtexGeneBedV8.bed
 
 # TODO: Add to gene sorter
 
-
+# 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   | 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 -tab bigBedInput.bed /cluster/data/hg19/chrom.sizes clinsub.bb
+ln -s `pwd`/clinsub.bb /gbdb/hg19