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tasks/TNseq.wdl
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| --algo TNhaplotyper2 $SAMPLE \ | --algo TNhaplotyper2 $SAMPLE \ | ||||
| --germline_vcf ${germline_resource} \ | --germline_vcf ${germline_resource} \ | ||||
| ${sample_id}.TNseq.raw.vcf \ | ${sample_id}.TNseq.raw.vcf \ | ||||
| --algo OrientationBias \ | |||||
| --algo OrientationBias --tumor_sample ${tumor_name} \ | |||||
| ${sample_id}.orientation \ | ${sample_id}.orientation \ | ||||
| --algo ContaminationModel $SAMPLE \ | --algo ContaminationModel $SAMPLE \ | ||||
| --vcf ${germline_resource} \ | --vcf ${germline_resource} \ |
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