A SNPs amd Alleles question

[IonMike]

Hello

I am trying to understand reading SNPs in relation to Alleles. I've used Samtools to generate the list of SNPs, but given there are 2 alleles I am thinking the result represents just a variant in one Allele?

What would display if the same SNP was present in both Alleles?

Thankyou in advance for any help you can provide.

[dpryan]

Samtools will try to determine whether the variant is homo- or heterzygous and indicate that in the VCF file it produces. You'll notice "0/1" for heterzygous and "1/1" for homozygous variants.

[IonMike]

Thanks for the quick reply but in my vcf output I am not seeing any 0/1's or 1/1's. I'm thinking you are referring to the GT information.

I'm using fileformat=VCFv4.0 and it's not displaying the GT information. Perhaps I've missed a setting to display this?

I've read elsewhere if AF1=1 then it is homozygous and also if FQ is negative but the author of that information was not getting consistent results between those 2 methods.

Is either of the AF or FQ information reliable? Or is there a setting I need to include to get the GT information in my results? Or something else?

Regards