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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Wrong annotation with Funcotator 1.7

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    A. Brink

    I've done some additional tests.

    - Also when using the v1.7.20200521g germline datasource the annotation mistakes are there.

    - Also when I run the Funcotator command without the -L and -ip options the annotation screwup is there.

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    A. Brink

    And more tests:

    - When first lifting my vcf file from hg19 to hg38 using GATK LiftoverVcf, and then running Funcotator using the v1.7.20200521g germline datasource with --ref-version hg38 results in output that is correct, and comparable to the v1.6 with --ref-version hg19.

    - The annotation output seems wrong for certain genes in my capture panel, some genes turn out to be fine.

    - For example, variants in HLA-A (chr6) and RB1 (chr13) are correctly annotated with  v1.6.20190124g hg19, v1.7.20200521g hg19 and v1.7.20200521g hg38. In contrast, variants in NOTCH1 (chr9) and TP53 (chr17) are correctly annotated with v1.6.20190124g hg19 and v1.7.20200521g hg38, but wrongly annotated when using v1.7.20200521g hg19.

     
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    Genevieve Brandt (she/her)

    Hi A. Brink, were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.

    If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.

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