1 gewijzigde bestanden met toevoegingen van 3 en 3 verwijderingen
+ 3
- 3
tasks/annovar.wdl
Bestand weergeven
| @@ -20,13 +20,13 @@ task annovar { | |||
| /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ | |||
| ${annovar_database} -buildver ${hg} \ | |||
| -out ${basename} -remove \ | |||
| -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 \ | |||
| -protocol refGene,ensGene,knownGene,rmsk,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,r,f,f,f,f,f,f,f,f,f,f,f,f,f \ | |||
| -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 | |||
| # --gff3dbfile hg38_rmsk.gff \ | |||
| #-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 \ | |||
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