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BamUtil: dedup

36 bytes added, 22:30, 14 April 2016
Implementation Notes
Rules:
* Skip Unmapped Reads, they are not marked as duplicate
* Reads whose mate is unmapped are treated as single-end
* 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 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:

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