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Old 06-30-2010, 01:07 PM   #1
Location: Philadelphia, PA

Join Date: Jun 2009
Posts: 16
Default Quality recalibration

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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bam, gatk, recalibration

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