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==Handling Recalibration/Implementation Notes==
==Handling Recalibration/Implementation Notes==
Recalibration is a 2-step process that loops through the file twice:
Recalibration is a 2-step process that loops through the file twice (stdin is not support as input):
# Build Recalibration Table
# Build Recalibration Table
# Apply Recalibration Table
# Apply Recalibration Table
NOTE: GATK ignores/skips adapters, but our logic does not.
NOTE: GATK ignores/skips adapters, but our logic does not.
== How to use it ==
== How to use it ==
== Required Generic Parameters ==
== Required Generic Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile|noStdin=1}}
{{outBAMOutputFile}}
{{outBAMOutputFile}}
