GATK: -I parameter in RealignerTargetCreator

jorge · 10-18-2011, 02:41 AM

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

ulz_peter · 10-18-2011, 03:35 AM

As far as I know the -I Argument is your input BAM file...

jorge · 10-18-2011, 04:10 AM

Ok Thanks,

I'll use my input bam file

Jorge

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10-18-2011, 02:41 AM	#1
jorge Member Location: Madrid, Spain Join Date: Jun 2011 Posts: 25	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

10-18-2011, 03:35 AM	#2
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	As far as I know the -I Argument is your input BAM file...

10-18-2011, 04:10 AM	#3
jorge Member Location: Madrid, Spain Join Date: Jun 2011 Posts: 25	Ok Thanks, I'll use my input bam file Jorge