Annotate using funcotator

July 27, 2023 18:56

I am trying to use :
./gatk Funcotator \
--variant variants.vcf \
--reference Homo_sapiens_assembly19.fasta \
--ref-version hg19 \
--data-sources-path funcotator_dataSources.v1.2.20180329 \
--output variants.funcotated.vcf \
--output-file-format VCF

But I want to use a zebra fish genome. Can you help me edit this code to suit my model system?

6 comments

Official comment
Jonn Smith

August 04, 2023 17:55
Rami Kheireddine

Funcotator is designed for users to create their own datasources to annotate their own favorite species and genes / other markers. The pre-packaged datasources are only for humans and were created for convenience, but are not required to make Funcotator work.

Unfortunately, right now there is a bug that prevents this from easily being done. We are working on fixing this so that users can create their own datasources for any species. We expect to have this fixed very soon.

To get up and running quickly, your best bet is to use a different tool.
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SkyWarrior

July 28, 2023 12:45
Hi Rami Kheireddine

I am not sure if there is any available zebra fish resources for Funcotator. You may wish to compile one for yourself but I would suggest you try Snpeff or Variant Effect Predictor for this purpose. Both tools have wide variety of resources to annotate zebrafish genome.
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Rami Kheireddine

July 28, 2023 14:14
Do you know what the format of the file should be?
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SkyWarrior

July 28, 2023 14:21

Edited
You may want to download and see it yourself. There is no single file format for this resource and some require internet connection.

gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521.tar.gz

Again my recommendation would be to use Snpeff or VEP.
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Sam

December 17, 2023 10:12

Edited
Hello,

Was the bug (preventing datasources for non-model organisms being easily created) fixed?

I am interested in annotating a non-model organism (germline usecase) based on the GTF (and fasta) file - wold you recommend Funcotator, or an alternative tool at this stage?
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Jonn Smith

December 18, 2023 13:51
Hi Sam,

The most recent release of GATK (4.5.0.0) has some fixes for funcotator that may have addressed this issue (in particular, the parsing for GTF/GFF3 files was updated). If you want, you can try to make some non-model organism datasources and see how well it works.

Thanks,

-Jonn
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