Funcotator table format

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vctrymao

• February 16, 2021 19:47

Is it possible to use Funcotator for germline calls but format the output in a table format instead of a VCF? I understand that MAF isn't yet available for germline Funcotator, but is there any other way to convert the VCF output into a table format?

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  Genevieve Brandt (she/her)

  • February 17, 2021 18:08

  Hi vctrymao,

  Please see the tool docs for Funcotator, MAF format is available but unsupported. So, you could try it anyway.

  I am not sure if it would work, but you could also check out the VariantsToTable GATK Tool to convert your VCF to a table.

  Best,

  Genevieve

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