0853d1cdfb0165451ebf726bc0579602ba756002
chmalee
  Thu Nov 16 09:19:31 2023 -0800
gnomAD fixed their chrY variants for their v4 release, add them in, refs Max email, #32545

diff --git src/hg/makeDb/doc/hg38/gnomad.txt src/hg/makeDb/doc/hg38/gnomad.txt
index 8eef883..eb5cda9 100644
--- src/hg/makeDb/doc/hg38/gnomad.txt
+++ src/hg/makeDb/doc/hg38/gnomad.txt
@@ -236,24 +236,24 @@
 # for each vcf in the download  dirs, install files into /gbdb and load up a table with the pointers
 gbdbPath="/gbdb/hg38/gnomAD/v4/"
 dataPath="/hive/data/outside/gnomAD.4/"
 for tbl in exomes genomes
 do
     mkdir -p ${gbdbPath}${tbl}
     ln -s ${dataPath}${tbl}/*.vcf.bgz* ${gbdbPath}${tbl}
     cp /dev/null ${tbl}.txt
     if [ ${tbl} == "exomes" ]; then
         for c in {1..22} X Y
         do
             f=${gbdbPath}${tbl}/gnomad.exomes.v4.0.sites.chr${c}.vcf.bgz
             echo -e "${f}\tchr${c}" >> ${tbl}.txt
         done
     else
-        for c in {1..22} X
+        for c in {1..22} X Y
         do
             f=${gbdbPath}${tbl}/gnomad.genomes.v4.0.sites.chr${c}.vcf.bgz
             echo -e "${f}\tchr${c}" >> ${tbl}.txt
         done
     fi
+    tName="${tbl^}"
+    hgLoadSqlTab hg38 gnomad${tName}V4 ~/kent/src/hg/lib/bbiChroms.sql genomes.txt
 done
-hgLoadSqlTab hg38 gnomadGenomesV4 ~/kent/src/hg/lib/bbiChroms.sql genomes.txt
-hgLoadSqlTab hg38 gnomadExomesV4 ~/kent/src/hg/lib/bbiChroms.sql exomes.txt