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