Changes

NOTE: This tool does not properly work on templates that have more than 2 segments.  It does not properly match reads when more than 2 reads have the same read name.

NOTE: This tool does not properly work on templates that have more than 2 segments.  It does not properly match reads when more than 2 reads have the same read name.

Potential future features:

Potential future features:

Rules:

Rules:

* Skip Unmapped Reads, they are not marked as duplicate

* Skip Unmapped Reads, they are not marked as duplicate

* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:

* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:

*# A paired-end record has the same key (even if the pair is not proper/the mate is unmapped/the mate is not found)<br/>-OR-

*# A paired-end record has the same key (even if the pair is not proper/the mate is not found)<br/>-OR-

*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])

*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])

* Mark both Paired-End Reads Duplicate if:

* Mark both Paired-End Reads Duplicate if:

   

   

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==

==Handling Recalibration==

== Required Parameters ==

== Required Parameters ==

{{inBAMInputFile}}

{{inBAMInputFile|noStdin=1}}

Note: The input file must be sorted by coordinate.

Note: The input file must be sorted by coordinate.

* supplementary reads

* supplementary reads

The Deduper will not work if secondary or supplementary reads are not excluded.  It will not properly find the mates since there will be more than 2 reads with the same mate information.

Secondary (0x100) and Supplementary (0x800) reads currently must be excluded.

=== Turn on Verbose Mode (<code>--verbose</code>) ===

=== Turn on Verbose Mode (<code>--verbose</code>) ===