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, 17:59, 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 <span style="color:red">TBD - this parameter is not yet implemented.</span>. | + | 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. |
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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. |
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| = Return Value = | | = Return Value = |