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varfish-org / mehari

VEP-like tool for sequence ontology and HGVS annotation of VCF files
MIT License
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Annotation of merged Sniffles 2 VCF files does not work. #357

Closed holtgrewe closed 7 months ago

holtgrewe commented 7 months ago

Describe the bug Annotating merged Sniffles 2 VCF files gives an error.

To Reproduce See below for a transcripts

> 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.multi.vcf --path-output-tsv test.tsv
2024-02-09T13:24:54.181726Z  INFO Mehari startup -- letting the dromedary off the leash...                                   
2024-02-09T13:24:54.181755Z  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.multi.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,
}
2024-02-09T13:24:54.181794Z  INFO Loading HGNC map ...
2024-02-09T13:24:54.216160Z  INFO ... done loading HGNC map
2024-02-09T13:24:54.216501Z  INFO Loading pedigree...
2024-02-09T13:24:54.216736Z  INFO ... done loading pedigree
2024-02-09T13:24:54.216745Z  INFO Open VCF and read header
2024-02-09T13:24:54.220964Z  INFO Determined input assembly to be Grch38
2024-02-09T13:24:54.220973Z  INFO Opening frequency database
2024-02-09T13:24:54.249820Z  INFO Opening ClinVar database
2024-02-09T13:24:54.258946Z  INFO Opening transcript database
2024-02-09T13:24:55.340737Z  INFO Building transcript interval trees ...
2024-02-09T13:24:55.388625Z  INFO ... done building transcript interval trees
2024-02-09T13:24:55.388643Z  INFO Annotating VCF ...
Error: Parsing Error: Error { input: "<DEL>", code: TakeWhile1 }

Expected behavior Annotation should succeed.

Additional context N/A