Base Quality values in BAM file

donniemarco · 06-22-2011, 09:09 AM

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 · 06-22-2011, 09:46 AM

samtools view bamfile.bam | cut -f11

donniemarco · 06-22-2011, 10:06 AM

Thanks for the reply!!!

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06-22-2011, 09:09 AM	#1
donniemarco Member Location: USA Join Date: Aug 2009 Posts: 17	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 !!

06-22-2011, 09:46 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	samtools view bamfile.bam \| cut -f11

06-22-2011, 10:06 AM	#3
donniemarco Member Location: USA Join Date: Aug 2009 Posts: 17	Thanks for the reply!!!