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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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vcf-converter error #136

Closed 2007lab closed 7 months ago

2007lab commented 1 year ago

Log file shows these errors 2023/02/09 10:04:09 cravat.converter liftover from hg19 2023/02/09 10:04:11 cravat.converter input format: vcf 2023/02/09 10:04:12 cravat.converter Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/cravat/cravat_convert.py", line 523, in run converter.addl_operation_for_unique_variant( File "/usr/local/lib/python3.10/dist-packages/cravat/modules/converters/vcf-converter/vcf-converter.py", line 347, in addl_operation_for_unique_variant oc_val = ','.join(map(tmp, info_val)) TypeError: 'bool' object is not iterable 2023/02/09 10:04:33 cravat.converter error lines: 93 2023/02/09 10:04:33 cravat.converter finished: Thu Feb 9 10:04:33 2023 2023/02/09 10:04:33 cravat.converter num input lines: 407 2023/02/09 10:04:33 cravat.converter runtime: 22.518 2023/02/09 10:04:33 cravat num_workers: 11 2023/02/09 10:04:34 cravat input line chunksize=37 total number of input lines=407 number of chunks=11

kmoad commented 1 year ago

This is likely an issue with the VCF headers. Issues like this can occur if a VCF header mislabels a value type as per-allele instead of per-variant.

If you're able to share the vcf, we might be able to find the offending line. Please email it to support@opencravat.org if you're not comfortable sharing it here.