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eastgenomics / eggd_generate_variant_workbook

DNAnexus app for generating xlsx variant workbooks
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Raise nicer error message on non-VEP annotated VCFs / handle non-VEP VCFs #117

Closed jethror1 closed 5 months ago

jethror1 commented 1 year ago

Currently only supports VEP annotated VCFs and will raise the following error on a non VEP annotated VCF being passed:

AssertionError: 
        Error in splitting VCF with bcftools +split-vep. VCF: 38_test_input_myeloid.vcf
        Exitcode:255
        The tag INFO/CSQ not found in the header
Failed to read from standard input: unknown file type

Can add a check to vcf.bcftools_preprocess() to call vcf.parse_header() and check if ##INFO=<ID=CSQ is present (and also if it has already been split with bcftools +split-vep).

This would also allow skipping this and should allow handling non-VEP annotated / unannotated VCFs but would require testing

jethror1 commented 5 months ago

Fixed in #172