Funcotator does not work on hg19

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Yosef Maruvka

• February 09, 2021 14:06

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:

gatk-4.1.8.1 

b) Exact command used:

gatk Funcotator \

     --variant /storage/bfe_maruvka/maruvka/6f0057fb-61b7-4a45-8cbd-75289fe8f791.vcf \

     --reference /storage/bfe_maruvka/References/New_hg19/Homo_sapiens_assembly19.fasta \

     --ref-version hg19 \

     --data-sources-path dataSourcesFolder/funcotator_dataSources.v1.6.20190124s \

     --output test6.MAF \

     --output-file-format MAF\

c) Entire error log:

No log error

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?

Non- of the above.

It just annotated every variant as IGR.  When I run it on H38 it worked well. I took the reference file from the google-cloud bucket. 

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• 

  Genevieve Brandt (she/her)

  • February 09, 2021 17:02

  Hi Yosef Maruvka,

  Your issue looks similar to a bug that we recently solved: https://github.com/broadinstitute/gatk/issues/7051

  Forum Post with more information.

  A solution for this will be in the next GATK release which will be within the next couple weeks. If you want to use it sooner, you can use the GATK nightly release from docker or build gatk from the master branch at github.

  Let me know if this is not the same issue you are seeing and we can look into your issue.

  Best,

  Genevieve

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