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I am working on using reads from regions that are not traditionally mapped(telomere), and am wondering about the GATK quality recalibration. As I understand it does so on an aligned BAM file. Are there reads that do/are not mappped in an aligned BAM file, and are these recalibrated also? Thanks, Nick |
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Warning: I'm a user, not a developer. With that said, CountCovariates is a LocusWalker so it will not see unmapped reads and the calibration table will only be based on data from mapped reads. TableRecalibrationWalker is a ReadWalker so it will update the quality scores for all reads based on the calibration data. Given that your data is telomeric (highly repetitive), I'd be a little apprehensive about using the recalibration utility - your data may have lots of mismatches due to mutations, not to sequencing errors, which could skew the recalibration as it doesn't really fit the model of how the recalibrator works. |
