GATK select variants

doc.ramses

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Join Date: Jan 2011

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#1

GATK select variants

10-14-2011, 12:30 AM

Hi,

assume I have 2 .vcf files from 2 individual samples which I would like to combine with GATK CombineVariants function. Then I would like to filter in a way that I end up only with variants that are present in both samples e.g. through GATK SelectVariants function. Or is there a better way ? Can anyone tell me how to do this ?

Thanx !
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swbarnes2

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#2

10-14-2011, 10:31 AM

BEDTools can take vcfs as input, and output the overlap. Or the ones that don't overlap.
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doc.ramses

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#3

10-18-2011, 03:41 AM

Oh, of course - thanks for bringing me on track again! :=)
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