Comments (3)
susannasiebert
commented on August 21, 2024
Would you be able to share your VCF with us? This error usually indicates a mismatch between the header definition and the contents of one of the VCF fields (i.e., some data is not in the format that is specified by its header line). I would need to debug your VCF to figure out which field specifically is the problem.
In regards to your installation question: sudo pip3 install vatools did not work for you? Can you please give me some more information on the installation steps you took?
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arumds
commented on August 21, 2024
The issue is with the VCF file. It has some missing fields in some rows. It works now after fixing the VCF.
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susannasiebert
commented on August 21, 2024
Glad to hear that. I'll close this issue.
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Related Issues (20)
- Enhancement: Adding allele counts per strand in vcf-readcount-annotator HOT 1
- warn when pick flag is expected but not observed
- Add feature to vcf-genotype-annotator to allow for adding GT field to existing samples
- Inaccurate warning message when running vcf-expression-annotator
- Bug in "vcf-genotype-annotator" due to misspelling HOT 1
- vcf-readcount-annotator only annotates first variant for indel HOT 1
- getting error when The INFO field name to use HOT 4
- When running the vcf-info-annotator support input TSVs with multiple value columns
- AttributeError: 'bool' object has no attribute 'split' HOT 2
- ref_transcript_mismatch_reporter: `ValueError: invalid literal for int() with base 10: '71/98'`
- VAtools vcf-expression-annotator does not add gene expression for genes without annotated gene names HOT 2
- small special bug about logging
- Installation via pip requires version previous than 21 because of Python version HOT 2
- vcf-readcount-annotator HOT 3
- VEP entry for at CHR chr*, POS *, REF *, ALT * already exists HOT 2
- ValueError: invalid literal for int() with base 10 HOT 1
- Support for GZ compressed annotation files
- Please consider adding support for multi-thread support HOT 3
- Support gene names as well as gene Ensembl IDs when using the `custom` option of the `vcf-expression-annotator` HOT 4
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