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Old 10-14-2011, 01:30 AM   #1
doc.ramses
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Default GATK select variants

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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Old 10-14-2011, 11:31 AM   #2
swbarnes2
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BEDTools can take vcfs as input, and output the overlap. Or the ones that don't overlap.
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Old 10-18-2011, 04:41 AM   #3
doc.ramses
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Oh, of course - thanks for bringing me on track again! :=)
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