Cis mapping¤

Cis mapping tests variants within a window around each molecular phenotype and reports one selected association per phenotype. The output includes the lead variant, its nominal association, and a gene-level adjusted p-value.

The --window value defaults to 500,000 bases. By default, the interval extends from TSS - window through TES + window. Add --tss-centered to instead use TSS - window through TSS + window.

Choose a calibration method¤

Use --spa --acat for fast score-test aggregation without permutations; SPA is strongly recommended because ACAT is sensitive to variant p-value calibration. Omit --acat to use Beta permutation, with --nperm controlling the number of shuffles. The methods need not produce the same p-values or discoveries. See Tests and gene-level calibration for the statistical tradeoffs.

The Quickstart contains complete commands for both methods.

Select regions and phenotypes¤

Use --chr LABEL to restrict the scan to an exact chromosome label shared by the inputs, and --gene-list PATH to select phenotype IDs from a file. Identifier lists contain one ID per line. Using a gene list with the full phenotype matrix preserves library-size offsets computed before gene selection; see Offsets when the input file itself has already been restricted.

Execution and fitting¤

Score and SPA scans reuse one null fit per phenotype; permutation scans fit a null model for each shuffle. Compiled kernels are reused across cis-window sizes. See Run large scans for compilation and memory behavior.

GLM fitting is controlled by --tol, --gtol, --max-iter, and --step-size. See Troubleshooting for defaults and stopping rules.

Inspect results¤

Follow Post-process cis results to filter failures and apply study-level FDR correction. The gene-level pvalue_adj is not an across-gene FDR value.

Genes with no variants in the requested window or no phenotype variance are skipped. See Cis output for the complete result contract.

See the Mapping command reference for all options and defaults.