Update: hg38_rmsk.gff

tasks/annovar.wdl

@@ -20,13 +20,14 @@ task annovar {
     /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
     ${annovar_database} -buildver ${hg} \
     -out ${basename} -remove \
-    -protocol refGene,ensGene,knownGene,rmsk,esp6500siv2_all,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \
-    -operation g,g,g,r,f,f,f,f,f,f,f,f,f,f,f,f,f \
+    -protocol refGene,ensGene,knownGene,esp6500siv2_all,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \
+    -operation g,g,g,f,f,f,f,f,f,f,f,f,f,f,f,f \
+    --gff3dbfile hg38_rmsk.gff \
     -nastring . -vcfinput -thread $nt
     fi
 
     # 1000g2015aug contains 6 datasets: ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08
-
+    
     #-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 \