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, 14:18, 3 July 2012
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| * Base is a CIGAR Match/Mismatch | | * Base is a CIGAR Match/Mismatch |
| * Previous base is a CIGAR Match/Mismatch or it is the first cycle | | * Previous base is a CIGAR Match/Mismatch or it is the first cycle |
| + | * Base position is not a dbSNP position |
| + | * Previous base position is not a dbSNP position (if not first cycle) |
| + | * Base quality > 5 (or the configurable minimum) |
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− | The Recalibration Table is applied on all bases in the read sequence (ignoring the alignment/CIGAR). If the base or the pre-base are an 'N', average the 4 alternatives. | + | The Recalibration Table is applied on all bases in the read sequence (ignoring the alignment/CIGAR) unless the base quality is < 5 (or the configurable minimum) |
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| + | This recalibration logic was designed for recalibrating ILLUMINA data. |
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| == How to use it == | | == How to use it == |