Funcotator to search in NCBI rather than Ensemble Database

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osman doluca

• August 04, 2024 09:06

Hello.

I am using GATK version 4.6.0.0

I want Funcotator to allign variants on to NCBI Transcripts (ie. NM000xxx) rather than Ensembl transcripts (ENST000xxx). Is it possible?

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  Gökalp Çelik

  • August 05, 2024 13:19

  Hi osman doluca

  Can you check the funcotation gencode_xrefseq in funcotator output? That field includes the NM transcript matching the Ensembl one used in annotation.

  I hope this helps.

  Regards. 

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