I have used Mutect2 to call somatic variants in the HLA region. Since I had the HLA type for my samples, I aligned the reads for each sample to a reference consisting of the type-specific HLA allele genomic sequences (from IMGT-HLA) for that sample. Thus my called variant locations refer to these specific alleles (e.g. CHROM: pos = HLA06606:5223).
I would like to use Funcotator to classify my calls (SILENT, MISSENSE, etc.). I'm not clear if this is possible. I thought I could provide a data source consisting of a gtf file with the exon/utr information for these specific HLA allele. However, the documentation at https://gatk.broadinstitute.org/hc/en-us/articles/360035889931#1.1.5 appears to indicate that gtf files are only acceptable for datasources from GENCODE and one needs to provide a specific ncbi build whose choices are limited (screenshot below). Is there a way I can achieve my goal, if not with gtf with another of the allowed file formats?
# Required field for GENCODE files. # NCBI build version (either hg19 or hg38): ncbi_build_version =
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