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tasks/VEP.wdl
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| # vcf2maf | # vcf2maf | ||||
| perl ${vcf2maf_path}/vcf2maf.pl \ | perl ${vcf2maf_path}/vcf2maf.pl \ | ||||
| --inhibit-vep | |||||
| --inhibit-vep \ | |||||
| --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \ | --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \ | ||||
| --tumor-id ${tumor_id} --normal-id ${normal_id} \ | --tumor-id ${tumor_id} --normal-id ${normal_id} \ | ||||
| --ref-fasta ${ref_dir}/${fasta} \ | --ref-fasta ${ref_dir}/${fasta} \ |
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