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Old 10-18-2011, 02:41 AM   #1
jorge
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Default GATK: -I parameter in RealignerTargetCreator

Hello all,

I trying to run GATK RealignerTargetCreator prior to the IndelRealigner.

The RealignerTargetCreator takes as the -I parameter a sample BAM file. Does anybody know what does the sample BAM file is for? Can I use a generic file for all the analyses?

any help will be apprecited.

Thanks
Jorge
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Old 10-18-2011, 03:35 AM   #2
ulz_peter
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As far as I know the -I Argument is your input BAM file...
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Old 10-18-2011, 04:10 AM   #3
jorge
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Ok Thanks,

I'll use my input bam file

Jorge
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