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Old 06-22-2011, 09:09 AM   #1
donniemarco
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Default Base Quality values in BAM file

I want to extract base (calls) quality values from BAM file.

I think these base quality value for each position are present in BAM file as there as Recalibration tool from GATK that uses them. Any trick or script?

Thanks !!
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Old 06-22-2011, 09:46 AM   #2
Richard Finney
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samtools view bamfile.bam | cut -f11
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Old 06-22-2011, 10:06 AM   #3
donniemarco
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Thanks for the reply!!!
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