REQUIRED for all errors and issues:
a) GATK version used:

Funcotator Version=4.1.9.0

b) Exact command used:

Funcotator --output out.vcf --ref-version hg38 --data-sources-path .../Funcotator/funcotator_dataSources.v1.7.20200521s --output-file-
format VCF --variant not_annotated.vcf
--reference genome.fasta --disable-sequence-dictionary-validation true --remove-filtered
-variants false --five-prime-flank-size 5000 --three-prime-flank-size 0 --force-b37-to-hg19-reference-contig-conversion false --transcript-selection-mode CANONICAL --lookahead-cache-bp 100000 --min-num-bases-for-segment-funcotation 150
--interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --create-output-bam-index true --create-output-bam-md5
false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-ba
m-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  
--disable-tool-default-read-filters false

When running Funcotator on the same not annotated file, we get differing output for some variants in the VCF and in the MAF file:

MAF output:

 Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
chr11      118436656    118436657                -                 -                 G
                         Genome_Change   cDNA_Change Protein_Change Variant_Classification
g.chr11:118436656_118436657insGGGGG c.144_145insG        p.G52fs        Frame_Shift_Ins
   Annotation_Transcript
ENST00000534358.8

VCF output:

chr11   118436656       .       TGGC    GGGGG (selected FUNCOTATION:) FRAME_SHIFT_INS  g.chr11:118436656_118436657insGGGGG  ENST00000534358.8  c.144_145insG

Notice the differing REF and ALT output between MAF and VCF. I was also wondering, why the cDNA change is only insG.

Best regards,

Balthasar