Add trans_geno_chromosome parameter and improve trans-QTL pipeline#1310
Merged
gaow merged 1 commit intoStatFunGen:mainfrom Apr 9, 2026
Merged
Add trans_geno_chromosome parameter and improve trans-QTL pipeline#1310gaow merged 1 commit intoStatFunGen:mainfrom
gaow merged 1 commit intoStatFunGen:mainfrom
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- Add `--trans-geno-chromosome` parameter to specify a different genotype chromosome for trans analysis, enabling phenotype chrX vs genotype chrY analysis - Support both single .bed/.pgen file (filter variants by chromosome after loading) and manifest file (load chromosome-specific plink file) modes - Update trans output filename: `_chrX_geno_chrY.trans_qtl` when trans_geno_chromosome is set, `_chrX.trans_qtl` otherwise - Fix region_list parsing in trans step to support comment lines, no header, and tab-separated format - Remove --entrypoint from help output Note: when running trans analysis split by chromosome (e.g. phenotype chr1 x genotype chr2, phenotype chr1 x genotype chr3, etc.), the q-values computed per-run are NOT accurate because they are based on a subset of tests. The q-values need to be recalculated after combining all results across runs. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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--trans-geno-chromosomeparameter to specify a different genotype chromosome for trans analysis, enabling phenotype chrX vs genotype chrY analysis_chrX_geno_chrY.trans_qtlwhen trans_geno_chromosome is set,_chrX.trans_qtlotherwiseNote: when running trans analysis split by chromosome (e.g. phenotype chr1 x genotype chr2, phenotype chr1 x genotype chr3, etc.), the q-values computed per-run are NOT accurate because they are based on a subset of tests. The q-values need to be recalculated after combining all results across runs.