Question: Vcf: How To Indicate Reference Allele Not Found?
gravatar for Nick Stoler
5.6 years ago by
Nick Stoler70
Penn State
Nick Stoler70 wrote:

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."

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?

vcf variant-calling • 1.7k views
ADD COMMENTlink modified 5.5 years ago by Adam990 • written 5.6 years ago by Nick Stoler70
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

The VCF spec says:

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

ADD COMMENTlink written 5.6 years ago by Pierre Lindenbaum121k

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?

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Nick Stoler70
gravatar for Adam
5.5 years ago by
United States
Adam990 wrote:

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

ADD COMMENTlink written 5.5 years ago by Adam990

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.

ADD REPLYlink written 5.5 years ago by Adrian Pelin2.3k
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