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Old 02-08-2012, 08:02 AM   #1
memento
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Default How to quickly rewrite MAQ calls in bam file

I was wondering if there is any swift solution to this problem. I am using bowtie to align my reads and it turns that all MAQ=255. This in turn causes GATK to drop all my calls.
GATK suggested to rewrite bam file with new MAQ scores (lets say 60).
-rf ReassignMappingQuality -DCQ 60 is discontinued for GATK1.4 and older versions (<1.4) return "exception faults". Any ideas ?
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Old 02-08-2012, 09:19 AM   #2
memento
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if anyone would be interested here is solution (at least it worked for me):

java -jar GenomeAnalysisTK.jar -T PrintReads -rf ReassignMappingQuality -DMQ 60 -R reference.fasta -I input.bam -o output.bam
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