Update: hg38-clinvar

tasks/annovar.wdl

@@ -15,11 +15,21 @@ task annovar {
     nt=$(nproc)
 
     if [ ${hg} == "hg38" ]; then
-    /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+    /installations/annovar/table_annovar.pl ${vcf} \
+    ${annovar_database} -buildver ${hg} \
+    -out ${basename} -remove \
+    -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20210501 \
+    -operation g,r,r,f,f,f,f,f,f,f \
+    -nastring . -vcfinput -thread $nt
     fi
 
     if [ ${hg} == "hg19" ]; then
-    /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+    /installations/annovar/table_annovar.pl ${vcf} \
+    ${annovar_database} -buildver ${hg} \
+    -out ${basename} -remove \
+    -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 \
+    -operation g,r,r,f,f,f,f,f,f \
+    -nastring . -vcfinput -thread $nt
     fi
   >>>