I have this variant given to me written as:
1:26697274:GCCA:CCCC
I think this is a "deletion and insertion" (is that a used term?) and this can be seen in the browser here
I don't think this would be validly written in VCF as:
CHROM POS REF ALT
1 26697274 GCCA CCCC
If I understand the VCF specification correctly we want to include the base before the variation as an achor, so if I wanted to harmonize the above 1:26697274:GCCA:CCCC to VCF spec, I would have to look that up the previous base with a software, which I think would translate to this:
CHROM POS REF ALT
1 26697273 CGCCA CCCCC
Is that right?
It looks like they do have an anchor for both insertion and deletion in the example 5.1.1
#CHROM POS ID REF ALT QUAL FILTER INFO
20 3 . C G . PASS DP=100
20 2 . TC T . PASS DP=100
20 2 . TC TCA . PASS DP=100
This is a really dumb question, but is my example and insertion-deletion, while the 5.1.1 example details one insertion and one deletion (both with anchors)
I guess you're right, they do have an anchor base for insertions as well, which in a way makes sense. More often than not, you see deletions where you see insertions so in the above example, callers would call the locus like so:
20 2 . TC T,TCA
In any case, go with what the specifications say. Use the additional anchor base.
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