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Old 09-06-2012, 09:46 AM   #1
bwubb
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Default GATK Input as list of BAMs

GATK documentation states the -I arguement can be List[String], which when using HaplotypeCaller or UnifiedGenotyper would produce a multisample vcf.

However, I am confused as to how exactly I present my list of bam files.

I attempted to just do:

-I path/to/bam1 path/to/bam2 path/to/bam3 etc.



Can anyone explain how to present multiple bams to GATK at once? Thank you.
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Old 09-06-2012, 10:35 AM   #2
behavin
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You'll need to create a text file where each line is your "path/to/bam.bam" . and then name it with a ".list" at the end ( ie. passing it to GATK as -I pathtobams.list)
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Old 09-06-2012, 10:46 AM   #3
bwubb
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I see, thank you very much!
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Old 09-06-2012, 11:37 AM   #4
vivek_
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If you have less than say 5 bams and rather list them in the command line you could also use -I bam1 -I bam2 -I bam3...
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