Posted in Ask the GATK team | Last updated on 2013-08-20 15:40:47

Comments (15)

Hi I am using this version of GATK which is java -jar /apps1/gatk/GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar

I have obtained my bam files using bowtie as aligner. So the quality score is 255 in the 5th column. I want to use UnifiedGenotyper and when i use it it gives me an error saying MappingQualityUnavailable.

So I see read filter ReassignOneMappingQualityFilter which can convert 255 to 60 and then it would be easily taken by UnifiedGenotyper to do the snp calling.

So what command line should i be using

This page is not telling how to provide input file and then output file

I have just started to explore GATK. Hope to hear from you soon

Regards Varun

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