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In The Vcf Format What Is The Correct Way To Represent An Insertion That Cannot Be Positioned (Missing Pos Column)

Hi all,

The VCF 4.1 file format specification states that the POS field is required. But suppose that you compare two genomes, a reference and an assembly, and find a big insertion in the assembly that you can't map to the reference unambiguously. Let me show an example. Let's denote by signed numbers large conservative regions (synteny blocks).

Reference is: +1 +2 +3 +2 +4 Assembly is: -1 +3 +4 -2 +5 -2

You see that +5 is a unique sequence that is not homologous to any sequence in the reference. But due to rearrangements, it's very hard to find the actual position of +5 in the reference. This situation is very common in bacteria, even within the same species (different strains). What is a proper way to report it in VCF?

P.S. VCF validator from vcftools doesn't permit '.' in the POS column.

vcf
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updated by Biostar Biostar • written by ilya.minkinen • ilya.minkinen

I don't think VCF is designed for your use case.

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written by lh3 lh3

Which solution would you suggest? A custom file format for such cases? Or it could be reasonable to extend VCF format for this?

• 9 views • link
written by ilya.minkinen • ilya.minkinen

Thank you, Jeremy, it is a very interesting link!

• 0 views • link
written by ilya.minkinen • ilya.minkinen

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