fi | fi | ||||
perl /opt/mskcc-vcf2maf/vcf2maf.pl \ | perl /opt/mskcc-vcf2maf/vcf2maf.pl \ | ||||
--input-vcf ${input_vcf} --output-maf ${basename}.maf \ | |||||
--input-vcf $input_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} \ | ||||
--vep-path ${vep_path} \ | --vep-path ${vep_path} \ |