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Funcotator error: Only IGRs were produced for this dataset

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    Anthony Dias-Ciarla

    Hi Mina,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out. I recognize that you are in a rush, so let us see what we can do.

    Firstly, it looks like you are not using the most up-to-date version of Funcotator data sources; please find the latest version below.

    funcotator_dataSources.v1.7.20200521s.tar.gz

    It also appears that there may be some inconsistencies between your references. I brought the issue you encountered to our developers; they provided the following suggestions.

    1. Try comparing your sequence dictionary in your vcf file to that of the hg38 reference that we use: (gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta)
    2. Specifically, try looking for whether your contigs have the chr prefixes.

    I hope this helps! Please let me know if this leads you to success. If not, I'll return this to the developers for the next steps.

    Best,

    Anthony

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    Mina

    Hi Anthony

    Thank you kindly for your response. I also use the latest version data sources (v1.7) but still got the same error. I think the problem is the format of my hg38 reference (GCF_000001405.40_GRCh38.p14_genomic.fna).  In the VCF file the "CHROM" column has refseq name of chromosomes (such as NC_000001.11). I  changed chromosome names in VCF file with prefix of chr by bcftools but it didn't help and I still get the same error.

    Just to note I didn't encounter any problems with this reference in previous steps such as (alignment with BWA or variant calling with Mutect2)

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    Anthony Dias-Ciarla

    Hi Mina,

    Thank you for your much-appreciated patience! I brought this back to our developers; they have some follow-up questions and things for you to try.

    1. Did you update the sequence dictionary in addition to the vcf header after changing chromosome names to chr?
    2. Did you re-index after you edited the CHROM call in the vcf?

    In the vcf header, there should be declarations for all the contigs; if the sequence dictionary is not also updated, you will encounter the same problem because GATK uses the sequence dictionary. Furthermore, if you do not re-index after editing the vcf, the index likely does not have the updated names. 

    Please try to verify that all are consistent and then attempt to re-run. I hope this helps bring you across the finish line! If not, please let me know, and we will figure out our next steps.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Mina,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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