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Fix reversed snpid allele order in VEP tutorial - #197
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The tutorial variants CSV stores genome-correct ref/alt values, but snpid used GWAS-style chrom:pos_ALT_REF ordering (with alt listed before ref), which made alleles look reversed relative to the IDs. Rebuild snpids as chrom:pos_REF_ALT and show ref before alt. Library code is unchanged. Fixes Genentech#33
avantikalal
approved these changes
Sep 17, 2026
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Summary
snpidvalues looked inconsistent with theref/altcolumns.ref/altcolumns match the hg19 reference; the mismatch came from GWAS-stylechrom:pos_ALT_REFsnpids (andaltlisted beforeref).snpidaschrom:pos_REF_ALTand reorders columns to the usualref,altorder after load. Stored notebook outputs updated accordingly.grelu.variantalready treatsref/altcorrectly.Test plan
refcolumn, not the first allele in the old snpid.docs/tutorials/5_variant.ipynbtables: snpids read…_REF_ALTand align withref/alt.