color-chrs-pl

name	color-chrs-pl
description	Use when rendering `bcftools +color-chrs` `.dat` output into an SVG chromosome-coloring plot, optionally with custom haplotype colors.
disable-model-invocation	true
user-invocable	true

color-chrs-pl

Quick Start

• Command: color-chrs.pl -p output-prefix output.dat
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/color-chrs.pl
• Help: perl /home/vimalinx/miniforge3/envs/bio/bin/color-chrs.pl -h
• Output: writes <prefix>.svg

When To Use This Tool

• Plot .dat files produced by bcftools +color-chrs.
• Build a chromosome-level SVG summary of haplotype assignments or painted regions.
• Apply a custom chr hap color palette instead of the built-in red / green / blue / yellow defaults.
• Combine multiple .dat files into one rendered figure when they belong in the same visualization.

Common Patterns

# 1) Render a basic plot from one plugin output file
color-chrs.pl -p sample sample.dat

# 2) Override the default haplotype colors
color-chrs.pl -c colors.txt -p sample sample.dat

# 3) Merge multiple .dat inputs into one SVG
color-chrs.pl -p cohort cohort_a.dat cohort_b.dat

Recommended Workflow

1. Generate one or more .dat files with bcftools +color-chrs.
2. Decide whether the default colors are acceptable or whether you need an explicit color map file.
3. Pick a unique -p prefix for the output figure before running the plotter.
4. Open the resulting <prefix>.svg and confirm the chromosome names and painted regions look sensible.

Guardrails

• -p is mandatory; omitting it aborts with Expected -p option.
• Help is available with -h, -?, or --help; there is no --version path in this script.
• File arguments are detected by existence, so typos are treated as unknown options while real existing paths are consumed as input files wherever they appear on the command line.
• The colors file must be whitespace-delimited chr hap color rows.
• The plotter hard-codes chromosomes 1 through 22 plus X, so it is not a natural fit for arbitrary contig naming or non-human assemblies.