Changes

==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 ==