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Fix reversed snpid allele order in VEP tutorial - #197

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buyan-kh:fix/vep-tutorial-ref-alt
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Fix reversed snpid allele order in VEP tutorial#197
buyan-kh wants to merge 1 commit into
Genentech:mainfrom
buyan-kh:fix/vep-tutorial-ref-alt

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@buyan-kh

@buyan-kh buyan-kh commented Sep 8, 2026

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Summary

  • Fixes Ref and alt reversed in VEP tutorial #33: in the VEP / variant-effect tutorial, snpid values looked inconsistent with the ref/alt columns.
  • Confirmed against dbSNP/NCBI that the CSV ref/alt columns match the hg19 reference; the mismatch came from GWAS-style chrom:pos_ALT_REF snpids (and alt listed before ref).
  • Tutorial now rebuilds each snpid as chrom:pos_REF_ALT and reorders columns to the usual ref, alt order after load. Stored notebook outputs updated accordingly.
  • No library code changesgrelu.variant already treats ref/alt correctly.

Test plan

  • Cross-checked several tutorial variants (e.g. rs138940043, rs66957194) against NCBI: genome REF matches the ref column, not the first allele in the old snpid.
  • Confirmed no open PR already targeting Ref and alt reversed in VEP tutorial #33.
  • Spot-check rendered docs/tutorials/5_variant.ipynb tables: snpids read …_REF_ALT and align with ref/alt.

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
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Ref and alt reversed in VEP tutorial

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