Question: Identifying private and shared SNPs using VCFtools
1
gravatar for outlier95
3.1 years ago by
outlier9510
outlier9510 wrote:

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

vcftools snps • 3.2k views
ADD COMMENTlink modified 11 months ago by Jorge Amigo11k • written 3.1 years ago by outlier9510
1
gravatar for RamRS
3.1 years ago by
RamRS23k
Houston, TX
RamRS23k wrote:

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

ADD COMMENTlink written 3.1 years ago by RamRS23k

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by outlier9510

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

ADD REPLYlink written 3.1 years ago by RamRS23k

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

ADD REPLYlink written 3.1 years ago by outlier9510
1
gravatar for Jorge Amigo
11 months ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Jorge Amigo11k
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