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, 18:06, 3 July 2012
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| == Minimum Recalibration Base Quality (<code>--minBaseQual</code>) == | | == Minimum Recalibration Base Quality (<code>--minBaseQual</code>) == |
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− | When recalibrating reads, only positions with a base quality greater than this minimum will be recalibrated. If <code>--minBaseQual</code> is not specified, it is defaulted to 5. | + | When recalibrating reads, only positions with a base quality greater than this minimum phred quality will be recalibrated. If <code>--minBaseQual</code> is not specified, it is defaulted to 5. |
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| The ILLUMINA specs indicate that any quality below 5 can be used as an error indicator so we do not want to recalibrate those. | | The ILLUMINA specs indicate that any quality below 5 can be used as an error indicator so we do not want to recalibrate those. |
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| + | == Maximum Recalibration Base Quality (<code>--maxBaseQual</code>) == |
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| + | This value sets the maximum phred base quality assigned to a base after recalibrating. Any qualities above this value will be set to this value. It is defaulted to 50. |
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| + | == Logistic Regression == (<code>--recabLogReg</code>) == |
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| + | Use the logistic regression empirical qualities for setting the new base qualities instead of the default formula: -10 * log10((#mismatches+1)/(#total+1)) |
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| + | == Read the quality from a tag (<code>--qualField</code>) == |
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| + | If this parameter is set, then read the quality string from the specified tag name. If the tag is not found, the quality is read from the quality field. |
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| + | == Store the original quality (<code>--storeQualTag</code>) == |
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| + | If this parameter is set, the original quality will be stored as a string in the specified tag. |
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| = Return Value = | | = Return Value = |