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With-chip optimization options : --chip-none, --chip-mix [ON],
With-chip optimization options : --chip-none, --chip-mix [ON],
--chip-refBias, --chip-full
--chip-refBias, --chip-full
BAM analysis options : --ignoreRG, --noEOF, --precise,
BAM analysis options : --ignoreRG, --ignoreOverlapPair,
--noEOF, --precise, --minMapQ [10],
--maxDepth [20], --minQ [13],
--maxQ [40], --grid [0.05]
Modeling Reference Bias : --refRef [1.00], --refHet [0.50],
Modeling Reference Bias : --refRef [1.00], --refHet [0.50],
--refAlt [0.00]
--refAlt [0.00]
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
* --free-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)
* --noEOF : do not check the EOF marker of the BAM file (for earlier version of BAM)
* --noEOF : do not check the EOF marker of the BAM file (for earlier version of BAM)
* --precise : calculate the likelihood in log-scale for high-depth data (recommended when --maxDepth is greater than 20. Can be a little bit slower)
* --precise : calculate the likelihood in log-scale for high-depth data (recommended when --maxDepth is greater than 20. Can be a little bit slower)
