Identifying private and shared SNPs using VCFtools

Question

[outlier95]

I want to identify private and shared polymorphisms between two .vcf files (or multi-sample vcf) using VCFtools. Any suggestions would be great. Thanks.

Answer 1

[Jorge Amigo]

update: bcftools isec does exactly these kind of comparisons, and faster. this quick example

bcftools isec -p isec_results file1 file2

generates in a isec_results folder vcf files with private variants from file1, private variants from file2, file1 variants shared with file2, and file2 variants shared with file1. these 2 last ones allow keeping file1 or file2 annotations respectively.

Answer 2

[Ram]

You could use vcf-contrast and vcf-isec to find unique and shared variants. The former works on a single VCF file, the latter with multiple VCF files. I'd play around with them until a better solution can be found.

• vcf-isec: http://vcftools.sourceforge.net/perl_module.html#vcf-isec
• vcf-contrast: http://vcftools.sourceforge.net/perl_module.html#vcf-contrast

[outlier95]

Could you please provide a simple example using vcf-contrast or vcf-isec to get me started? Thanks.

[Ram]

There are examples with explanations in the link. Do you have a specific question?

[outlier95]

I see that now :). I will try and report back if I have any issues. Thanks again...