1 changed files with 2 additions and 1 deletions
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tasks/TNseq.wdl
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| --tumor_segments ${sample}.contamination.segments \ | --tumor_segments ${sample}.contamination.segments \ | ||||
| ${sample}.contamination | ${sample}.contamination | ||||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \ | |||||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \ | |||||
| -r ${ref_dir}/${fasta} \ | |||||
| --algo TNfilter \ | --algo TNfilter \ | ||||
| --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ | --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ | ||||
| -v ${sample}.TNseq.TN.tmp.vcf \ | -v ${sample}.TNseq.TN.tmp.vcf \ |
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