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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Funcotator: all Clinvar fields blank #8963

Open gevro opened 2 weeks ago

gevro commented 2 weeks ago

Hi, With the latest version of gatk 4.6.0 and the latest funcotator v1.8 annotation, all Clinvar fields are returning blank, even though there are many variants that I know are in clinvar. Seems like a bug. Thanks

ClinVar_VCF_AF_ESP|ClinVar_VCF_AF_EXAC|ClinVar_VCF_AF_TGP|ClinVar_VCF_ALLELEID|ClinVar_VCF_CLNDISDB|ClinVar_VCF_CLNDISDBINCL|ClinVar_VCF_CLNDN|ClinVar_VCF_CLNDNINCL|ClinVar_VCF_CLNHGVS|ClinVar_VCF_CLNREVSTAT|ClinVar_VCF_CLNSIG|ClinVar_VCF_CLNSIGCONF|ClinVar_VCF_CLNSIGINCL|ClinVar_VCF_CLNVC|ClinVar_VCF_CLNVCSO|ClinVar_VCF_CLNVI|ClinVar_VCF_DBVARID|ClinVar_VCF_GENEINFO|ClinVar_VCF_MC|ClinVar_VCF_ORIGIN|ClinVar_VCF_RS|ClinVar_VCF_ID|ClinVar_VCF_FILTER

gokalpcelik commented 2 weeks ago

How did you download the funcotator resources? Did you use the official download tool?

gevro commented 2 weeks ago

I downloaded it manually from the official Google cloud bucket. And I see the Kinar folders. And the files are getting annotated with clinvar columns, except they're all empty.

gevro commented 2 weeks ago

Looks like the chromosome names are 1, 2, 3, instead of chr1, chr2, chr3 in the supplied clinvar resource. Maybe that is the issue?

Note, I'm finding multiple other issues with the Funcotator 1.8 resources.

  1. Separate issue: #8965
  2. The Funcotator download tool for 1.8 creates an empty directory clinvar_hgmd. Not sure what that is?
  3. The Funcotator 1.8 somatic extracted folder on the google bucket does not have the dna_repair_genes folder that is created by the Funcotator download tool. Suggests a discrepancy between the extracted folder on the google bucket vs the tar.gz file in the google bucket.

I think it might help for someone from the Funcotator team (@jamesemery ?) to review all the resources again, or perhaps there is something I'm doing wrong.