Annotate using funcotator
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?
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Official comment
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.
Comment actions -
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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Do you know what the format of the file should be?
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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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