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* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence-only method
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence-only method
* --chip-none : Do not perform sequence+array method to estimate parameters
* --chip-none : Do not perform sequence+array method to estimate parameters
* --free-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
* --chip-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
* --free-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
* --chip-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
* --chip-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
* --ignoreRG : ignore the read grouup level comparison and compare samples only (recommended for an expedited run)
* --ignoreRG : ignore the read grouup level comparison and compare samples only (recommended for an expedited run)
* --ignoreOverlapPair : ignore overlapping pair end fragment covering the same base. Disabling this option may decrease the sensitivity of the method when the insert size is short (with slight gain in the computational speed)
* --ignoreOverlapPair : ignore overlapping pair end fragment covering the same base. Disabling this option may decrease the sensitivity of the method when the insert size is short (with slight gain in the computational speed)
