vcf file filtering looking for polimorphisms

[Danielbenitezr]

Hi everyone:

I recently got my mpileup-bcftools results looking for SNV's on a ~200 sample population. It happens that there is no reference genome for this species, so I used a taxonomic close-related one for the reads mapping. The thing is that, in my vcf file, there are a lot of variants that were called just because of the diferences between my samples and the reference, but there is no difference between any of my samples. All the genotypes are called as the same in a lot of loci. So I need to filter my vcf file then, by the presence of polimorphisms between my samples. Is there a tool to manage this?



thanks!!

[AdrianP]

You got your 200 samples so that you could look at variation among these samples, not variation of these samples to a close reference, correct?

You need to try a denovo assembly of one of your samples, get decent contigs, and do analysis on that.

[Danielbenitezr]

Thanks Adrian,

So... there's no way to do what I wanted to do? Because it's not possible to try a denovo assembly; the proyect i'm working for does not include that methodology so I have to try to do it anyway.

=/


Any other idea?

thanks again!

[Danielbenitezr]

I'll try to use vcf-compare:

http://vcftools.sourceforge.net/perl_module.html#vcf-compare

but I will have to generate a .vcf file for every one of my samples

I'll let you know what happens