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Old 01-20-2014, 10:24 AM   #1
frz
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Default Filtering over 10 vcf files

Hi there, does anyone know a tool where I can compare more than 2 vcf files at once? I have 10 samples and I want to get common variants among them. I can run Bedtools -IntersectBed 5 times, comparing one to one and that to the other and so on, or try vcf -isec and do the same multistep process. But I'd like to also know if there are subsets within the 10 that I might miss with my method. For example a variant that is common to 7 samples only but not all 10. I couldn't find that by my method as it would depend a lot on the order I do the filtering in.
Any help or suggestions?
Many thanks
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Old 01-20-2014, 10:41 AM   #2
blakeoft
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It looks like VCFtools' vcf-compare does what you want it to do:

http://vcftools.sourceforge.net/perl...ml#vcf-compare
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Old 01-23-2014, 10:19 AM   #3
frz
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Thanks! yes, from the description it should work. I've been trying to install and run vcf tools but haven't managed to do it yet. Can't seem to find a good guide to the vcf install.
I guess there is no simpler way to do this? I've compiled a concatenated file of all my variants that has a sample name column. I am trying to sort by gene name and then pull out all genes that for each gene name, have all sample names...
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