Incorrect Annotation from Funcotator
Answered
Hi,
In a project of mine, I used funcotator to annotate somatic mutations using the following command:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /wynton/home/cbi/shared/software/CBI/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar funcotator --data-sources-path /wd/funcotator_dataSources.v1.7.20200521s -R /wd/ucsc.hg19_M_1_22_X_Y.fasta --ref-version hg19 -V /wd/SC300025_new.vcf -O SC300025.maf --output-file-format MAF.
However, the annotation result does not exactly match the ANNOVAR annotation. Therefore we checked a few different annotations in IGV and found that the funcotator gave the incorrect protein change.
For example, this is one of the PKD1 mutation I identified with funcotator:
But in fact the protein change should be: p.L2169S.
Could you please help me figure out the root cause for this and how to remedy this? This issue is troubling me because not all the annotations are off (most are correct) so it is difficult to systematically identify the incorrect ones.
Thanks!
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Hi Hanbing Song,
This is a known issue with the Funcotator 1.7 data sources and the version of GATK you are using. See the github ticket and another user's post. You can upgrade your GATK version to solve this issue!
Best,
Genevieve
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Thank you, Genevieve, for your response!
Yeah, I saw the other post before but since the gatk I am using now is curated by our computational cluster so I don't think I have enough permission to upgrade it. I am wondering if this could be solved by the new GATK version or something wrong with the funcotator data source.
Thanks!
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You can either download the 1.7 data sources with GATK version 4.2.0.0 or higher and this should be fixed, or you can use the 1.6 data sources with your current GATK version. If you can have your cluster upgrade the GATK version, the first option would be better because you would have more up to date data sources.
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Ah, got it! Thanks!
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You're welcome!
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