Re-key SNP to the harmonized variant id after panel harmonization#533
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.matchAgainstSketch rewrites variant_id to the panel allele orientation and sign-flips Z/BETA but left SNP at the input orientation. Kriging, z-mismatch QC, and the downstream fine-mapping LD lookup all key on SNP, so sign-flipped variants missed the panel: slalom/dentist/kriging errored and fineMappingPipeline dropped them. Sync SNP to variant_id after harmonization. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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.matchAgainstSketch rewrites variant_id to the panel allele orientation and
sign-flips Z/BETA but left SNP at the input orientation. Kriging, z-mismatch QC,
and the downstream fine-mapping LD lookup all key on SNP, so sign-flipped variants
missed the panel: slalom/dentist/kriging errored and fineMappingPipeline dropped
them. Sync SNP to variant_id after harmonization.
Co-Authored-By: Claude Opus 4.8 noreply@anthropic.com