Find common SNP in vcf files.

JdeBruin

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#1

Find common SNP in vcf files.

05-11-2015, 01:11 AM

Hi,

I have vcf files for 6 individuals and I would like to find SNP's that occur in all 6 vcf files. Any ideas how this can be done, I can write a script to do this but if it is been done I don't want to waste time. To note , I dont want to lose what the SNP call for each individuals, so I would like 6 vcf files one for each individual containing only SNP's that are present in the other lines.

Any help would be appreciated.
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GenoMax

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Join Date: Feb 2008

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05-11-2015, 01:18 AM

See if this would do. VCFtools: http://vcftools.sourceforge.net/

Usage: http://vcftools.sourceforge.net/man_latest.html

Last edited by GenoMax; 05-11-2015, 01:20 AM.
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JdeBruin

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#3

05-11-2015, 01:25 AM

I thanks, I am reading the VCF tools currently and I have used it. Was wondering if anyone has an command example that would achieve this.
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