Make rss_analysis.ipynb the GWAS RSS fine-mapping workflow#1378
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Ports the 4-step manifest -> construct -> fine_mapping -> plot workflow into rss_analysis.ipynb (replacing the legacy univariate_rss two-step) and removes the duplicate gwas_rss_fine_mapping.ipynb. Repoints the remaining doc references. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Ports the 4-step GWAS RSS workflow (manifest -> construct -> fine_mapping -> plot) into rss_analysis.ipynb, replacing the legacy univariate_rss two-step, and removes the now-duplicate gwas_rss_fine_mapping.ipynb. Repoints the four remaining doc references.
Depends on the pecotmr harmonization SNP re-key fix (branch harmonize-rekey-snp): the slalom/dentist/kriging QC modes need it to handle sign-flipped variants. Validated end-to-end on the protocol_example chr22 MWE — noQC and slalom+impute reproduce the legacy output/rss_analysis variant set and lead.