[E002] Contig validation failed ... Missing in VCF/FASTA
Contig names don't match between files. All inputs (VCF, FASTA, GFF) must use identical contig names (case-sensitive). Normalize names before running.
[E002] VCF REF/FASTA mismatch at <contig>:<pos>
The REF allele in VCF doesn't match the FASTA base at that position. Ensure the VCF was called against the same reference.
[E002] Invalid base 'X' in REF/ALT allele ...
Non-IUPAC base detected. Clean invalid alleles from the VCF before running.
Sample '<name>' not found in VCF header
Check sample name spelling, or omit --sample to use the first sample.
TSV annotation does not include contig names
TSV format has no contig column. Use --gff for multi-contig VCFs, or restrict with --chrom.
--strict enabled, but original VCF metrics are missing ...
Ensure each VCF record has recoverable DP and AF/FREQ in FORMAT or INFO fields.
Multiallelic VCF record ... is not supported
Either pre-split with bcftools norm -m - or run with --split-multiallelic.
| Error | Fix |
|---|---|
--index-vcf-gz requires --vcf-gz |
Enable BGZF output first |
--bcf requires --convert or --both |
Enable VCF output mode |
--keep-original-info requires --convert or --both |
Enable VCF output mode |
--min-strand-bias-p must be between 0 and 1 |
Use a value in [0, 1] |
Requested --sample all but input VCF has no sample columns
Use a VCF with FORMAT/sample columns, or omit --sample all.
| Code | Name | Description |
|---|---|---|
| 0 | Success | |
| 1 | Generic | Unclassified error (E000) |
| 2 | Config | CLI/configuration error (E001) |
| 3 | Validation | Input/validation error (E002) |
| 10 | I/O | File read/write error |
| 11 | CSV | CSV parsing error |
| 12 | HTSlib | BAM/VCF library error |
| 13 | UTF-8 | Encoding error |
| 14 | Parse | Data parsing error |