1 змінених файлів з 3 додано та 2 видалено
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tasks/annovar.wdl
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| /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ | /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ | ||||
| ${annovar_database} -buildver ${hg} \ | ${annovar_database} -buildver ${hg} \ | ||||
| -out ${basename} -remove \ | -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 \ | |||||
| -protocol refGene,ensGene,knownGene,rmsk,esp6500siv2_all,1000g2015aug,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \ | -protocol refGene,ensGene,knownGene,rmsk,esp6500siv2_all,1000g2015aug,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \ | ||||
| -operation g,g,g,r,f,f,f,f,f,f,f,f \ | -operation g,g,g,r,f,f,f,f,f,f,f,f \ | ||||
| -nastring . -vcfinput -thread $nt | -nastring . -vcfinput -thread $nt | ||||
| fi | fi | ||||
| #-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 \ | |||||
| if [ ${hg} == "hg19" ]; then | if [ ${hg} == "hg19" ]; then | ||||
| /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ | /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \ |
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