73ecf418edee1ae991841f9bbf6ec5fe623407ec
chmalee
  Fri Mar 1 15:24:02 2024 -0800
Staging gnomAD v4 constraint track on test, refs #33084

diff --git src/hg/makeDb/gnomad/combine.awk src/hg/makeDb/gnomad/combine.awk
index 10c6874..8c712ac 100755
--- src/hg/makeDb/gnomad/combine.awk
+++ src/hg/makeDb/gnomad/combine.awk
@@ -6,31 +6,34 @@
 # sort -k1,1 -k2,2 pliByTranscript.tab > pliByTranscript.bed
 # sort -k1,1 -k2,2 missenseByTranscript.tab > missenseByTranscript.bed
 #
 # The doTranscripts argument tells the script which accession to use as the name field
 # in the final beds, which is the ENST accession for by_transcript, and the ENSG accession for
 # by_gene. It also sets the output files name correctly {missense,pli}By{Gene,Transcript}.tab
 #
 BEGIN {
     FS="\t";
     OFS="\t";
     isTranscripts=doTranscripts
 }
 
 {
 chrom=$2
+gnomadChrom=$13
+if (substr($13, 1, 3) != "chr") {
     gnomadChrom=sprintf("chr%s", $13)
+}
 if (chrom != gnomadChrom) {
     # so far just the multiple mapping PAR regions
     printf "bad join: %s\n", $0 > "/dev/stderr"
     next
 }
 
 chromStart=$3
 chromEnd=$4
 missOutFile=""
 pliOutFile=""
 if (isTranscripts == "true") {
     name=$1
     missOutFile="missenseByTranscript.tab"
     pliOutFile="pliByTranscript.tab"
 } else {