v1.1.0

This release addresses a few bugs and introduces a couple of enhancements adding the possibility to select specific chromosomes for analysis and allowing better control over finemapping

Bug fixes

• fix a bug when both summary stats and bim file are in GRCh37 build and no liftover is requested (#95)
• correctly report as finemapping exceptions loci that are removed by finemapping QC (#91)
• update flandeRs R package to version 1.0.1, to avoid an error when shared credible-sets are found during the colocalization step. Now the pipeline will produce an empty guide table, and colocalization is skipped as expected.

Enchancements

• user can now select which chromosome to consider in the analysis using the chromosomes parameter (#86)
• refactor finemapping QC logic post SUSIE (see below)
• sdY can now be passed as a file reporting sdY for each trait (#85). This is useful when working with molecular traits, such as eQTLs

Refactored finemapping QC and SUSIE logic

1. Selective QC by L

Before: All loci (fine-mapped with either L=1 or L=10) were passed through post-SuSiE QC.

After:

• Only loci fine-mapped with L=10 undergo QC.
• Loci fine-mapped with L=1 are kept as-is (QC skipped).

2. Fallback strategy when QC removes all credible sets

Before: If all credible sets were removed by QC, the locus was silently dropped.

After:

• If QC removes all credible sets at L=10, the locus is re-fine-mapped with L=1 (and accordingly, QC is then skipped).
• Loci re-finemmaped at L=1 are reported in the finemapping_exceptions/FINEMAPPED_L1_recover_after_susie_QC.tsv file, stating "Locus re-finemapped at L=1 after none of the credible sets fine-mapped at L=10 passed post susie QC."

3. Switched from natural log to raw BF threshold

Before: BF threshold was passed as natural log Bayes factor and then converted to log₁₀ scale (log10(exp(cs_bf_thr)))
After: BF threshold is now passed as raw Bayes factor and then converted to log₁₀ scale (log10(cs_bf_thr))