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This code assumes that at most 1000 bases are clipped at the start of a read.
This code assumes that at most 1000 bases are clipped at the start of a read.
==Handling Recalibration==
Reads skipped for recalibrating (both for determining recalibrated values and for being modified):
* Duplicates
* Unmapped
* Mapping Quality = 0
== How to use it ==
== How to use it ==
The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
= Usage =
= Usage =
