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Add chr prefix to gnomAD.r2.1.1-sv.vcf.gz for svdb/query test - #2268
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ramprasadn merged 1 commit intoSep 11, 2026
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sv_query.vcf.gz (the query input in svdb/query's nf-test) uses chr-prefixed contig names (chr22), while this gnomAD SV database used bare names (22). svdb <= 2.8.4 silently normalized away chr prefixes on read, so the mismatch never mattered, but svdb 2.9+ dropped that normalization (J35P312/SVDB@a520684), so the two files no longer overlap and the query test's only annotated hit was silently lost. Align the naming so the fixture actually exercises a match.
beatrizsavinhas
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Sep 11, 2026
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Very nice description of the investigation! And great that you already checked that the file is not used for anything else too! 🌟
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Summary
gnomAD.r2.1.1-sv.vcf.gzused bare chromosome names (22) whilesv_query.vcf.gz(the query VCF used against it innf-core/modules'svdb/querytest) useschr-prefixed names (chr22). This mismatch means the two files describe the same genomic positions but never lexically match.svdb <= 2.8.4 silently stripped
chrprefixes on read, so the mismatch didn't matter in practice. svdb 2.9+ intentionally removed that normalization, so with svdb 2.12.0 the two files no longer overlap at all, and thesvdb/querytest's only annotated hit silently disappeared.This PR fixes that by adding
chrprefix tognomAD.r2.1.1-sv.vcf.gz's CHROM column,##contigheader IDs, andCHR2INFO values so it's consistent withsv_query.vcf.gz, restoring the intended annotation match under current and future svdb versions.This file is only referenced by
nf-core/modules'svdb/querytest, so this change is isolated.