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Thread Tools |
10-14-2011, 01:30 AM
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#1 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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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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10-14-2011, 11:31 AM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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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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10-18-2011, 04:41 AM
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#3 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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Oh, of course - thanks for bringing me on track again! :=)
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