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== Minimum Recalibration Base Quality (<code>--minBaseQual</code>) ==
== Minimum Recalibration Base Quality (<code>--minBaseQual</code>) ==
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.
The ILLUMINA specs indicate that any quality below 5 can be used as an error indicator so we do not want to recalibrate those.
= Return Value =
= Return Value =
