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tasks/TNseq.wdl
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| @@ -60,7 +60,8 @@ task TNseq { | |||
| --tumor_segments ${sample}.contamination.segments \ | |||
| ${sample}.contamination | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \ | |||
| -r ${ref_dir}/${fasta} \ | |||
| --algo TNfilter \ | |||
| --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ | |||
| -v ${sample}.TNseq.TN.tmp.vcf \ | |||
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