- Specify Diploid Chromosome: Normalize results to specified chromosome
- Median Normal Coverage: Median coverage value of SNPS from normal samples
- Minimum Scale Factor (autosomes): This value is multiplied by the median to compute the minimum coverage value
- Maximum Scale Factor (autosomes): This value is multiplied by the median to compute the maximum coverage value
- Minimum X Scale Factor: Minimum scale factor for chromosome X.
- Maximum X Scale Factor: Maximum scale factor for chromosome X.
- Sample Order (VCF Format Only): VCF input must include Tumor and Normal data following the FORMAT Field. Tumor/Normal assigns the Tumor data to the 1st field following FORMAT and Normal data to the 2nd field following FORMAT. Normal/Tumor is inverse.

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