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tasks/annovar.wdl
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| @@ -20,8 +20,8 @@ task annovar { | |||
| /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ | |||
| ${annovar_database} -buildver ${hg} \ | |||
| -out ${basename} -remove \ | |||
| -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 \ | |||
| -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,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,r,f,f,f,f,f,f,f,f,f,f,f,f,f \ | |||
| --gff3dbfile hg38_rmsk.gff \ | |||
| -nastring . -vcfinput -thread $nt | |||
| fi | |||
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