Annotation of GLNexus-merged Clair3 data does not work

[holtgrewe]

Describe the bug
Clair3 VCF files merged with GLNext cannot be annotated.

To Reproduce
See below for a transcript.

$ mehari annotate seqvars --path-db /data/cephfs-1/work/groups/cubi/projects/biotools/mehari/0.21.0/db/ --path-input-ped test.ped --path-input-vcf test.vcf --path-output-tsv test.tsv
2024-02-09T11:42:14.299911Z  INFO Mehari startup -- letting the dromedary off the leash...
2024-02-09T11:42:14.299953Z  INFO config = Args {
    path_db: "/data/cephfs-1/work/groups/cubi/projects/biotools/mehari/0.21.0/db/",
    genome_release: None,
    path_input_ped: "test.ped",
    path_input_vcf: "test.vcf",
    output: PathOutput {
        path_output_vcf: None,
        path_output_tsv: Some(
            "test.tsv",
        ),
    },
    transcript_source: Both,
    report_all_transcripts: true,
    transcript_picking: false,
    max_var_count: None,
}
2024-02-09T11:42:14.299999Z  INFO Loading HGNC map ...
2024-02-09T11:42:14.337259Z  INFO ... done loading HGNC map
2024-02-09T11:42:14.338766Z  INFO Loading pedigree...
2024-02-09T11:42:14.340157Z  INFO ... done loading pedigree
2024-02-09T11:42:14.340167Z  INFO Open VCF and read header
2024-02-09T11:42:14.343339Z  INFO Determined input assembly to be Grch38
2024-02-09T11:42:14.343349Z  INFO Opening frequency database
2024-02-09T11:42:14.372492Z  INFO Opening ClinVar database
2024-02-09T11:42:14.380959Z  INFO Opening transcript database
2024-02-09T11:42:15.489215Z  INFO Building transcript interval trees ...
2024-02-09T11:42:15.537581Z  INFO ... done building transcript interval trees
2024-02-09T11:42:15.537599Z  INFO Annotating VCF ...
Error: invalid genotypes

Caused by:
    0: invalid values
    1: invalid value
    2: invalid character

Expected behavior
Annotation must be possible.

Additional context
N/A

[holtgrewe]

Actually, it's a question of whether fixed-length character fields in VCF can be represented by fixed-length strings.

Also see:

• Fixed-length Character fields zaeleus/noodles#235
• Multiple characters are not a string... or are they? samtools/hts-specs#631
• RNC field not comma-separated dnanexus-rnd/GLnexus#306