kuva manhattan
Manhattan plot for GWAS results.
Input: chromosome, (optional) base-pair position, and p-value columns.
Two layout modes:
- Sequential (default): chromosomes are sorted and SNPs receive consecutive integer x-positions. Position column is not used.
- Base-pair (
--genome-build): SNP x-coordinates are resolved from chromosome sizes in a reference build.
| Flag | Default | Description |
|---|---|---|
--chr-col <COL> | 0 | Chromosome column |
--pos-col <COL> | 1 | Base-pair position column (bp mode only) |
--pvalue-col <COL> | 2 | p-value column |
--pvalue-col-is-log | off | p-value column already contains −log₁₀(p); un-transform before plotting |
--genome-build <BUILD> | — | Enable bp mode: hg19, hg38, or t2t |
--genome-wide <F> | 7.301 | Genome-wide threshold (−log₁₀ scale) |
--suggestive <F> | 5.0 | Suggestive threshold (−log₁₀ scale) |
--top-n <N> | 0 | Label N most-significant points above genome-wide threshold |
--point-size <PX> | 2.5 | Point radius |
--color-a <CSS> | steelblue | Even-chromosome color |
--color-b <CSS> | #5aadcb | Odd-chromosome color |
--legend | off | Show threshold legend |
# sequential mode (no position column needed)
kuva manhattan gene_stats.tsv --chr-col chr --pvalue-col pvalue --top-n 5
# base-pair mode
kuva manhattan gwas.tsv \
--chr-col chr --pos-col pos --pvalue-col pvalue \
--genome-build hg38 --top-n 10 --legend
# when p-value column already holds -log10(p)
kuva manhattan gwas.tsv --chr-col chr --pvalue-col neg_log10_p --pvalue-col-is-log
See also: Shared flags — output, appearance, axes, log scale.