1 changed files with 4 additions and 1 deletions
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tasks/charger.wdl
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| vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/.vcf//'` | vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/.vcf//'` | ||||
| echo ${sample_id} | echo ${sample_id} | ||||
| mkdir ./input/ | |||||
| mkdir ./output/ | mkdir ./output/ | ||||
| sed 's/chr//' ${vep_vcf} > ./input/${vep_index}.nochr.vcf | |||||
| charger -f ${vep_vcf} \ | |||||
| charger -f ./input/${vep_index}.nochr.vcf \ | |||||
| -o ./output/$vep_index.charger.tsv \ | -o ./output/$vep_index.charger.tsv \ | ||||
| -D --inheritanceGeneList ${inheritanceGeneList} \ | -D --inheritanceGeneList ${inheritanceGeneList} \ | ||||
| -l --mac-clinvar-tsv ${clinvar} \ | -l --mac-clinvar-tsv ${clinvar} \ |
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