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Old 01-02-2013, 06:03 AM   #9
priesgo
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Location: Spain

Join Date: Aug 2012
Posts: 22
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Let me retake this old issue.

I am working with 1000 genomes project alignments data and they have done their SOLiD alignment with bfast 0.64e, so I have two options: I redo the alignment myself with a newer version of bfast as it is said above; or I try to handle the 255 before GATK.

Handling the 255 mapping qualities requires replacing this values with something else in the interval [0, 254]. Any ideas on this?

I am trying to do it with samtools calmd mapping quality capping option.
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