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Export to VCF does not include symbolic non-ref if site has a called alt #1551

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fnothaft opened this Issue May 30, 2017 · 0 comments

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fnothaft commented May 30, 2017

If you call a variant at a site and also have non-reference model (<NON_REF>) likelihoods, we should emit that symbolic non-ref allele (along with the likelihoods). The current export code doesn't do this properly.

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