Changes

<span style="color:red">TBD - this parameter is not yet implemented.</span>

<span style="color:red">TBD - this parameter is not yet implemented.</span>

== BAM File Is Sorted By Read Name (<code>--minRecabQual</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>--minQual</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 <span style="color:red">TBD - this parameter is not yet implemented.</span>.

= Return Value =

= Return Value =