c248c85dafaa2167b3ad8e0ad76be7d4a9a05385
max
  Fri Oct 30 09:02:47 2020 -0700
lifting covid rare mutations to hg38 and polishing up the track a bit more, refs #26351

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 82ab2a2..65a998c 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33785,15 +33785,23 @@
 # update 2020-10-27 (DONE - Hiram - 2020-10-27)
 
   mkdir /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27
   cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27
 
   time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
       -bigClusterHub=ku -dbHost=hgwdev \
       -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \
       GCF_000001405.25_GRCh37.p13 hg19) > do.log 2>&1 &
   # real    6m47.005s
 
   cat fb.ncbiRefSeq.hg19.txt
   # 93720294 bases of 2991710746 (3.133%) in intersection
 
 #############################################################################
+# Covid-19 rare mutations, Max, Fri Oct 30 08:40:34 PDT 2020
+# received table from qzhang02@rockefeller.edu, wrote to UCSC.txt
+cd /hive/data/genomes/hg19/bed/covidMuts/
+dos2unix UCSC.txt
+cat UCSC.txt | tawk '{$1="chr"$1; chrom=$1; start=$2; rsId=$3; ref=$4; alt=$5; zygo=$6; gene=$7; genotype=$8; inh=$9; end=$2+length(ref); print chrom, start, end, ref">"alt, "0", ".", start, end, "0,0,0", "1", length(ref), "0", ref, alt, rsId, zygo, gene, genotype, inh;}' | grep -v chrchr > covidMuts.bed
+bedSort covidMuts.bed covidMuts.bed
+bedToBigBed -tab covidMuts.bed ../../chrom.sizes covidMuts.bb -as=../../hg19/bed/covidMuts/covidMuts.as -type=bed12+
+#############################################################################