共有 2 个文件被更改，包括 2 次插入 和 2 次删除
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defaults
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| "interval_padding": "100", | "interval_padding": "100", | ||||
| "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02", | "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02", | ||||
| "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3", | "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3", | ||||
| "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04", | |||||
| "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2019.10", | |||||
| "tnseq_pon": "", | "tnseq_pon": "", | ||||
| "tnscope_pon": "", | "tnscope_pon": "", | ||||
| "disk_size": "200", | "disk_size": "200", |
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tasks/annovar.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -hgvs -out ${annotated_vcf} -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} ${database} -buildver ${hg} -out ${annotated_vcf} -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 | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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