I am using graphtyper genotype with the --vcf flag to genotype a specific set of input variants. However, it seems that Graphtyper does not only genotype these variants, but in some cases comes up with other alleles for some of the variants.
As an example, I am genotyping the following variant:
5 12446876 . A AGAAAG
As output, Graphtyper gives me this:
5 12446876 5:12446876:IG A AGAAAG,AGAAAT 255 PASS [...] 2/2:0,0,15:1:16:45:255,255,255,45,48,0
I.e., Graphtyper suggests another allele AGAAAT and genotypes the variant as 0/2. The allele AGAAAT is not in the input vcf. I suspect this could happen if there is another insertion in the vcf, but in my case there is none.
Is this expected behaviour? If so, does this mean that Graphtyper does not only genotype the provided variants, but also does some kind of variant detection at the sites of the provided variants?
If needed, I can try to reproduce this behaviour on a smaller test data set that can be shared.
Hi!
I am using
graphtyper genotypewith the--vcfflag to genotype a specific set of input variants. However, it seems that Graphtyper does not only genotype these variants, but in some cases comes up with other alleles for some of the variants.As an example, I am genotyping the following variant:
As output, Graphtyper gives me this:
I.e., Graphtyper suggests another allele
AGAAATand genotypes the variant as 0/2. The alleleAGAAATis not in the input vcf. I suspect this could happen if there is another insertion in the vcf, but in my case there is none.Is this expected behaviour? If so, does this mean that Graphtyper does not only genotype the provided variants, but also does some kind of variant detection at the sites of the provided variants?
If needed, I can try to reproduce this behaviour on a smaller test data set that can be shared.