Liquid Tumor Calling

Liquid tumors in liquid tumor mode refer to hematological cancers, such as leukemia. In tumor-normal analysis, DRAGEN accounts for Tumor-in-Normal (TiN) contamination by running liquid tumor mode. You can use liquid tumor mode to account for TiN contamination by allowing a nonzero variant allele frequency for the matched normal when calculating the posterior probability of the somatic state. If the contamination is not accounted for, it can severely impact sensitivity by suppressing true somatic variants.

Use the following two options to control liquid tumor mode behavior.

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--sv-enable-liquid-tumor-mode—Enable liquid tumor mode. Liquid tumor mode is disabled by default.

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--sv-tin-contam-tolerance—Set the TiN contamination tolerance level. DRAGEN calls variants in the presence of TiN contamination up to a specified maximum tolerance level. You can enter any value between 0–1. The default maximum TiN contamination tolerance is 0.15. If using the default value, somatic variants are expected to be observed in the normal sample with allele frequencies up to 15% of the corresponding allele in the tumor sample.