Base Quality values in BAM file

[donniemarco]

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 !!

[Richard Finney]

samtools view bamfile.bam | cut -f11

[donniemarco]

Thanks for the reply!!!