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36 bytes added
, 22:30, 14 April 2016
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| Rules: | | Rules: |
| * Skip Unmapped Reads, they are not marked as duplicate | | * 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: | | * 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: |