Retrieval of similar positions from samples in a vcf but different from reference

Question

[bioinfo8]

Hi,

I have a vcf file (for "a" type of samples) a_filtered_ann10.vcf annotated for 10 genes by bcftools and consists of 5 samples and similarly b_filtered_ann10.vcf . I have visualized both the vcf files in IGV and can see the variation with respect to the reference.

Now, I would like to retrieve only those positions from each file which are similar among the samples but different from the reference.

Any guidance would be appreciated.

Thanks!

Answer 1

[guillaume.rbt]

Hi, If you want to get snps where all samples are different from the ref you can use SnpSift filter ( http://snpeff.sourceforge.net/SnpSift.html ) and filter on the genotype field.

[bioinfo8]

Thanks. SnpSift is part of SnpEff distribution and I tried annotating my variants using SnpEff but it showed error: unknown input vcf format and hence, I used bcftools for annotation (where I did not find such issue). Therefore, I want to use non-SnpEff based solution.

[microfuge]

Would bcftools view work if min alternate allele frequency is set to 1.0 ?

bcftools view --min-af 1 input.vcf.gz

[guillaume.rbt]

Maybe you can just filter all non variant genotypes of your vcf :

cat your_vcf.vcf | grep -v "0/0"

Then you will have only variants with all samples being homozygote or heterozygote.