vcf filtering

[doc.ramses]

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!

[quinlana]

Why not use those tools and intersect the file to itself?

[doc.ramses]

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 ?

[Bukowski]

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?

[doc.ramses]

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.