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This repository was archived by the owner on Apr 19, 2023. It is now read-only.
This repository was archived by the owner on Apr 19, 2023. It is now read-only.

Importing variants hangs with VEP consequence "start_retained_variant" #11

Description

@AlesMaver

Importing the VEP annotated vcf file using docker exec bravo_web_1 python manage.py variants hangs if "start_retained_variant" is present in the CSQ field.

Adding the consequence "start_retained_variant" to utils.py fixes the error:

    _other_csqs = [
        "coding_sequence_variant",
        "mature_miRNA_variant",
        "5_prime_UTR_variant",
        "3_prime_UTR_variant",
        "non_coding_transcript_exon_variant",
        "intron_variant",
        "NMD_transcript_variant",
        "non_coding_transcript_variant",
        "upstream_gene_variant",
        "downstream_gene_variant",
        "TFBS_ablation",
        "TFBS_amplification",
        "TF_binding_site_variant",
        "regulatory_region_ablation",
        "regulatory_region_amplification",
        "feature_elongation",
        "regulatory_region_variant",
        "feature_truncation",
        "start_retained_variant",
        "intergenic_variant",
    ]

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