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# MSI |
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# MSI |
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mkdir -p /cromwell_root/tmp/${sample} |
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mkdir -p /cromwell_root/tmp/${sample} |
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msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list |
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msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list |
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if [ ${normal_recaled_bam} ]; then |
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if [ ${normal_bam} ]; then |
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msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} |
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msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} |
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else |
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else |
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msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} |
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msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} |