VCF reference and alternative allele

Question

[onemoreuser]

I don't understand what are the reference and the alternative alleles in the vcf file format. Having a variant with reference='A' and alternative allele='C' and a genotype='0/0' means that the individual is 'A/A'? But in this case how the 'C' was found if the reference is 'A' and the individual is 'A/A'?

[GouthamAtla]

What is the source of VCF file ? How did you generate it ?

[waakurugu.akurugu]

I will really appreciate the answer to this question. I am working with vcf files and observing similar alternate alleles and genotypes

[finswimmer]

Hello onemoreuser and waakurugu.akurugu,

you should realy provide an example of your vcf file and descibe how it was produced.

I have two guesses:

1. You have more than one sample in your vcf file and at least one sample provide the alternate allele
2. Depending on the variant caller it might happen that the caller first suspect a variant at this position, but within a review process it discarded this as there were to less evidences. This should result in a (very) low QUAL value,

fin swimmer

[ATpoint]

You have more than one sample in your vcf file and at least one sample provide the alternate allele

Would also be my guess, but as said, provide some example data.

[GenoMax]

ATpoint : I am going to hijack this thread for a moment. You have been promoted to moderator status. I suggest that you join the biostars slack channel Inviting NEW Biostars moderators to join Biostars slack channel .