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Base Quality values in BAM file

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  • 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 !!

  • #2
    samtools view bamfile.bam | cut -f11

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    • #3
      Thanks for the reply!!!

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