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VCF file format

This is a follow up question to what I asked earlier today. Now, I see values for REF and ALT as follows:

REF: GAAAAAAAG
ALT: AAAAAAAAA

I really do not understand what sort of mutation this is trying to convey. Is this a valid code? I am at a loss as to how to interpret it...

Another one is:

Ref: ACT
Alt: TCC

Again, I am not sure what rule to apply here for interpretation.

vcf
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updated by Ram Ram • written by luca.pamparana • luca.pamparana

In both examples there are two changes (i.e. multiple nucleotide polymorphisms or MNP). In the first example, the both G's have changed to an A. In the second example, there is an A change to T and a T change to C.

C: Variant calling for MNP

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updated by Ram Ram • written by rbagnall rbagnall

These records are not as per VCF standards. (including the earlier records you have posted)

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written by cpad0112 cpad0112

Thanks for pointing that out. I am still getting familiar with it but I will try and check if I can find out more about the source.

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written by luca.pamparana • luca.pamparana

The output is probably from FreeBayes, which calls MNPs in addition to SNPs and indels.

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written by harold.smith.tarheel harold.smith.tarheel

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