load_maf does not convert UCSC contig names (GDC chr-prefixed MAFs fail annotation)
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 72/100
- Issue type
- Bug
- Clarity
- Clearly specified
- Activity status
- Active
- Tech stack
- python
- Domain
- bioinformatics
Research direction
Start in varcode/maf.py around line 212, where load_maf constructs each Variant, and compare with how load_vcf passes convert_ucsc_contig_names=True. Then check the VariantCollection.from_json path, which the issue says behaves the same way. Done means a test with a GDC-style chr-prefixed MAF produces annotated effects instead of Failure, and the chr-prefixed and unprefixed inputs give matching results.
Written by the indexing model from the issue text.
Description
load_maf builds each Variant without convert_ucsc_contig_names=True (varcode/maf.py ~212, varcode 11.3.1). GDC GRCh38 MAFs write Chromosome as chr7, so their variants keep the UCSC name and fail annotation. load_vcf and the CLI's --variant convert these names.
Seen through isovar on Sid osteosarcoma data (openvax/isovar#661):
isovar run --maf sid-three.maf …, withchr7,chr9andchr14andNCBI_Build GRCh38, collects and assembles every read, then fails withInvalidContigError: Invalid contig name 'chr14' for reference 'GRCh38'. The same MAF without thechrprefix works.isovar plot --mafexits 0 with an empty figure: no genes or transcripts, although it found 7 ALT reads. The only signal is two WARNINGs.VariantCollection.from_jsonwithchr7variants (isovar--json-variants) appears to behave the same: effectFailure, with a WARNING. Not root-caused.
Suggested fix: pass convert_ucsc_contig_names=True in load_maf (and check the JSON path), with a test on a GDC-style chr MAF.
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