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01-04-2012, 07:12 AM
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#1 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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vcf filtering
I have a multi sample vcf file. How can I filter only for overlapping snps within this one vcf file.
As far as I understand, intersectBed and vcf-isec only work for different files. Thanks a lot for your help! |
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01-04-2012, 08:01 AM
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#2 |
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Senior Member
Location: Charlottesville Join Date: Sep 2008
Posts: 119
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Why not use those tools and intersect the file to itself?
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01-04-2012, 11:40 AM
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#3 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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hm, but how can a target certain samples ? lets say I have a vcf with 10 samples. how to filter only for variants overlapping in samples 1 sample 3 and sample 7 ?
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01-04-2012, 12:15 PM
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#4 | |
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Senior Member
Location: UK Join Date: Jan 2010
Posts: 390
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01-04-2012, 12:23 PM
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#5 | |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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Quote:
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