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!!
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!!
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