Vcf: How To Indicate Reference Allele Not Found?

Question

[Nick Stoler]

In VCF, the ALT column is supposed be where you show what variants you found. Or, as implied in the spec and all the example files I've seen, the ALT column shows all the non-reference variants you found.

But if I'm sequencing a sample and want to use VCF to store its variant calls, I'd like to be able to explicitly say "I did find the REF allele here" and "I did not find the REF allele there."

tl;dr:
1) Is it valid to put the REF allele in the ALT column, and
2) regardless of validity, do common tools explode if they encounter this situation?

Answer 1

[Pierre Lindenbaum]

The VCF spec says: http://samtools.github.io/hts-specs/VCFv4.2.pdf

If there are no alternative alleles, then the missing value ('.') should be used

[Nick Stoler]

I noted that, though I wasn't sure how definitively that says "no REF alleles."

So then what is the appropriate format for storing this information? It seems like quite an achilles heel to not be able to list the alleles in your sample unambiguously. (I could use a hack like an INFO column tag or something, but that seems.. hacky.)

Also, any thoughts on tl;dr #2?

Answer 2

[Adam]

Why not use AF=1.0 in the INFO field? Or define a new INFO flag?

[Adrian Pelin]

that would make sense...

If you are working with bacteria or any haploid organism you looking at fixed alleles i guess.

If you are looking at diploid or polyploid beasts then you want homozygous SNPs? AF=1 works... so does RO=0, which means I did not find REF allele here.