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

fnothaft opened this issue May 30, 2017 · 0 comments
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0.23.0

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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.
@fnothaft fnothaft added the bug label May 30, 2017
@fnothaft fnothaft added this to the 0.23.0 milestone May 30, 2017
@fnothaft fnothaft self-assigned this May 30, 2017
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 7, 2017
@fnothaft
[ADAM-1551] Emit non-reference model genotype at called sites.
d26a6d5 
Resolves bigdatagenomics#1551.
@fnothaft fnothaft mentioned this issue Jun 7, 2017
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fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017
@fnothaft
[ADAM-1551] Emit non-reference model genotype at called sites.
7f20c73 
Resolves bigdatagenomics#1551.
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 22, 2017
@fnothaft
[ADAM-1551] Emit non-reference model genotype at called sites.
dfe1fe2 
Resolves bigdatagenomics#1551.
heuermh pushed a commit that referenced this issue Jun 22, 2017
@fnothaft @heuermh
[ADAM-1551] Emit non-reference model genotype at called sites.
2676112 
Resolves #1551.
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