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132 bytes added
, 11:17, 19 September 2012
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| *# 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: |
− | # Another paired-end pair has the same set of keys and has a higher base quality sum. | + | # Another paired-end pair has the same set of keys and has a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]]) |
| | | |
| 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. |