056e469252385766eda11785f44b081af9c69fa9
lrnassar
  Fri Feb 5 11:04:27 2021 -0800
Adjusting clinGen otto script to account for the 6 new fields added to the files, and adding the .as files to the git repo, no RM

diff --git src/hg/utils/otto/clinGen/makeDosage.sh src/hg/utils/otto/clinGen/makeDosage.sh
index 1e4d8a2..e7ee818 100755
--- src/hg/utils/otto/clinGen/makeDosage.sh
+++ src/hg/utils/otto/clinGen/makeDosage.sh
@@ -41,24 +41,24 @@
             grc="GRCh37"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_${grc}.tsv"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_${grc}.tsv"
         elif [ ${db} == "hg38" ]
         then
             grc="GRCh38"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_${grc}.tsv"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_${grc}.tsv"
         fi
         echo $grc
         # the process script creates a haplo.bed and triplo.bed file:
         hgsql -Ne "select phenotypeId, description from omimPhenotype" ${db} > ${db}.omimPhenotypes
         ../../../processClinGenDosage.py ClinGen_region_curation_list_${grc}.tsv ClinGen_gene_curation_list_${grc}.tsv ${db}.omimPhenotypes ../output/${db}
         sort -k1,1 -k2,2n ../output/${db}.haplo.bed > ../output/${db}.clinGenHaplo.bed
         sort -k1,1 -k2,2n ../output/${db}.triplo.bed > ../output/${db}.clinGenTriplo.bed
-        bedToBigBed -type=bed9+13 -as=../../clinGenDosageHaplo.as -tab ../output/${db}.clinGenHaplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenHaplo.bb
-        bedToBigBed -type=bed9+13 -as=../../clinGenDosageTriplo.as -tab ../output/${db}.clinGenTriplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenTriplo.bb
+        bedToBigBed -type=bed9+16 -as=../../clinGenDosageHaplo.as -tab ../output/${db}.clinGenHaplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenHaplo.bb
+        bedToBigBed -type=bed9+16 -as=../../clinGenDosageTriplo.as -tab ../output/${db}.clinGenTriplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenTriplo.bb
         cp ../output/${db}.clinGenHaplo.bb ${WORKDIR}/release/${db}/clinGenHaplo.bb
         cp ../output/${db}.clinGenTriplo.bb ${WORKDIR}/release/${db}/clinGenTriplo.bb
     done
     cd ../..
 else
     echo "No ClinGen CNV update"
 fi