3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Parameters
== 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 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.
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.
== Maximum Recalibration Base Quality (<code>--maxBaseQual</code>) ==
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.
== Logistic Regression == (<code>--recabLogReg</code>) ==
Use the logistic regression empirical qualities for setting the new base qualities instead of the default formula: -10 * log10((#mismatches+1)/(#total+1))
== Read the quality from a tag (<code>--qualField</code>) ==
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.
== Store the original quality (<code>--storeQualTag</code>) ==
If this parameter is set, the original quality will be stored as a string in the specified tag.
= Return Value =
= Return Value =
