Funcotator gnomAD MAF columns

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TMB

• August 23, 2021 02:04

Hi

I used Funcotator to annotate VCF (somatic variant calling). 

I am tying to filter out variants based on MAF and would like to use a female population (inclusive for all ancestries).  I have used the column, "gnomAD_exome_AF_female" for this purpose. Could someone give me more specific description of this particular column?  I want to be cognizant of ethnic differences and would like to make sure I am choosing the right column.

Thank you.  - TMB

 

Basic info - 
a) GATK version used: GATK4
b) Exact command used: Funcotator with default settings

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  Pamela Bretscher

  • August 23, 2021 13:50

  Hi TMB,

  The gnomAD files provided by the Broad are very ethnically diverse. Here is a link to an information page describing the creation and details for the gnomAD data. Specifically in the technical details section, under the header "What populations are represented in the gnomAD data", you can find the specific breakdown of ethnicity, gender, and exome/genome data present in the files. The column you are specifying would limit the filtration to the AF annotation for female exomes. You can see that this group contains a wide range of ancestries, and should therefore work for what you are trying to accomplish. Please let me know if this does not sufficiently answer your question.

  Kind regards,

  Pamela

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  TMB

  • August 23, 2021 14:54

  Thank you so much.  This is very helpful. 

  TMB

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