# Window Maker

> Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.

- Skill: `vimalinx/window-maker` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/window-maker`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/window-maker/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/window-maker

---


# window-maker

## Quick Start
- **Command:** `windowMaker [-g genome.txt | -b intervals.bed] [-w size | -n count] [options]`
- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/windowMaker`
- **Full reference:** See `references/help.md`

## When To Use This Tool

- Tile a genome or interval set into fixed-width windows.
- Create sliding windows by combining `-w` with `-s`.
- Split each source interval into a fixed number of windows with `-n`.
- Add window identifiers for downstream joins, coverage summaries, or matrix construction.

## Common Patterns

```bash
# 1) Make non-overlapping 1 Mb genome windows
windowMaker \
  -g genome.txt \
  -w 1000000
```

```bash
# 2) Make sliding 10 kb windows with 5 kb step
windowMaker \
  -g genome.txt \
  -w 10000 \
  -s 5000
```

```bash
# 3) Split each BED interval into 20 windows and label by window number
windowMaker \
  -b regions.bed \
  -n 20 \
  -i winnum
```

## Recommended Workflow

1. Choose the source domain first: whole-genome tiling with `-g` or per-interval tiling with `-b`.
2. Choose fixed width (`-w`) versus fixed count (`-n`) based on the downstream statistical design.
3. Add `-s` only when you intentionally want overlapping sliding windows.
4. Use `-i` and optionally `-reverse` when downstream tools need stable window IDs rather than anonymous coordinates.

## Guardrails

- You must provide one interval source: `-g` or `-b`.
- You must provide one windowing mode: `-w` or `-n`.
- `-s` is meaningful with `-w` window-size mode, not as a replacement for `-n`.
- The genome file is tab-delimited chromosome name plus size; a FASTA `.fai` works because bedtools reads only the first two columns.
- Prefer `-h` for help; GNU-style `--version` on this wrapper emits errors before exiting.