Comments (1)
Your VCF looks fine. But make sure that "tumor-id" exactly matches the name of the sample ID in your VCF column header for th genotype field. This is needed to extract the AD field which contains this data.
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Related Issues (20)
- --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410 HOT 2
- Losing info when reading maf file
- Add options for RefSeq and Merged caches when converting to MAF
- ERROR: Failed to run the VEP annotator! HOT 2
- Running error HOT 3
- Why is empty in all database? HOT 1
- Option --retain-fmt doesn't work
- ERROR: Provided --ref-fasta is missing or empty HOT 3
- Update vcf2maf to work with later Ensembl vep releases HOT 2
- Release new tag HOT 4
- ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID
- ERROR: Failed to run the VEP annotator!
- The best solution for one-to-one correspondence between genes and transcripts HOT 3
- VCF2MAF and allele frequency HOT 4
- cosmic annotation
- HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108 HOT 3
- Error Argument "" isn't numeric in subtraction HOT 2
- WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority! HOT 1
- Unrecognized biotype/effect HOT 2
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