Genome Analysis Toolkit

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

Funcotator Information and Tutorial Follow


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    Field -Ye Tian

    Dear GATK developers, 

    I have processed a pair of Tumor/normal tissues that are WES'ed. I have followed the whole process of analysis and acquired the annotated .maf result. After going through it, I didn't see a column that's dedicated to the credibility of each variant. 

    I recall that when I used the VarScan2, it assigned a P value for each variant. It is calculated somehow by the number of reads supporting either the reference or the alternate from both the tumor and normal samples. I wonder if Mutect2 did the same and if I missed it. 


    Thank you very much. 


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    David Lord

    I believe there is a typo in the README file in the v.1.7 somatic data source package. The "use case" clearly states "somatic", however, the introduction starts with: "This is a collection of data sources to be used in conjunction with Funcotator to annotate Germline data samples."

    Thank you for providing the pre-packaged data sources and the downloader tool, saved me a whole bunch of time! :) 

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    Lim Chen

    I tried to have funcotator annotate some germline variants. Here is my command in mac zshell terminal:

    lc % gatk Funcotator --variant ./chr3q.vcf --reference ./reference/GATK/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --ref-version hg38 --data-sources-path ./reference/GATK/funcotator/funcotator_dataSources.v1.7.20200521g --output chr3q_funcotated.maf --output-file-format MAF

    However, I ran into following error:

    A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths:

      contig reference = chr1 / 248956422

      contig features = chr1 / 249250621.


    I download both the fasta hg38 and funcotator data source bundle from GATK. I noticed that the contig reference chr1 / 248956422 is from hg38; while the contig features = chr1 / 249250621 actually match GRCH37 chr1 length shown in the following screenshot, which is hg19.  I specified in `--ref-version hg38`. What causes this error, and how to fix it?? I want to use hg38 because my variants are called using hg38 ref. Thanks for any help.



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    Jonn Smith

    Lim Chen

    We recommend that people create new posts in the general comments section for support questions.

    That said, I'm guessing your VCF is aligned to HG19 / B37.  VCF files have header rows in them that specify the reference dictionary used when calling the variants (among other things).  Are you sure you called your variants on HG38?

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