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pcingola / SnpEff

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"N" in ALT being changed to A,C,G,T - undesirable #54

Closed dandanxu closed 3 years ago

dandanxu commented 9 years ago

I'm having a problem where some of the records in my VCF files have a single N in the ALT field. SnpEff/SnpSift keeps changing these to A,C,G,Ts. Is there any way to turn this feature off in the future? Or for that matter, a feature that makes it so that SnpEff doesn't change anything in the original VCF record besides adding a INFO field.

Example: original VCF record, VCF record after SnpEff

1 123456    rs123  NTGTATT  N

1 123456    rs123  NTGTATT  A,C,G,T
pcingola commented 9 years ago

Hi, I'll try to get this issue fixed for the next release. Thank you for your bug report!

pcingola commented 3 years ago

Closing old issues.