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Old 01-04-2012, 07:12 AM   #1
doc.ramses
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Default 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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Old 01-04-2012, 08:01 AM   #2
quinlana
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Why not use those tools and intersect the file to itself?
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Old 01-04-2012, 11:40 AM   #3
doc.ramses
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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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Old 01-04-2012, 12:15 PM   #4
Bukowski
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Quote:
Originally Posted by doc.ramses View Post
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 ?
Why not use vcf-subset to leave the samples in separate vcf's and then use vcf-isec?
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Old 01-04-2012, 12:23 PM   #5
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Quote:
Originally Posted by Bukowski View Post
Why not use vcf-subset to leave the samples in separate vcf's and then use vcf-isec?
This is the solution I'm using, now. But with a growing sample number, this is really annoying. I thought there must be a more elegant one doing this in one step.
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