There are edge cases where vcfallelicprimitives doesn't always split apart indels and SNPs

[ernfrid]

I've encountered a case of an adjacent indel and SNP that were unable to be picked apart by vcfallelicprimitives. The variant is an T insertion into a T homopolymer run and an A->T SNP at the end of the run. A more complete representation would be: TTTTTTTTA -> TTTTTTTTT

The indel as reported is this: 5 132267859 . A TT

Running through vcfallelicprimitives doesn't change the representation at all, even though this is a SNP and an indel. Adding padding allows this to be split out as I would have expected.

5 132267858 . TA TTT is then reported as

5   132267858   .   T   TT
5   132267859   .   A   T

[travc]

Bump... I'm seeing cases like this too. It would be very nice if vcfallelicprimitives would handle them, since otherwise I just have to exclude such sites (with two variant types) from my downstream analysis.

[ekg]

Interesting issue. The fact that adding padding changes the output is a bit surprising.

On Tue, Dec 9, 2014 at 3:31 PM, Travis Collier notifications@github.com wrote:

Bump... I'm seeing cases like this too. It would be very nice if vcfallelicprimitives would handle them, since otherwise I just have to exclude such sites (with two variant types) from my downstream analysis.

— Reply to this email directly or view it on GitHub https://github.com/ekg/vcflib/issues/49#issuecomment-66352150.

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