kcftools increaseWindow¶
The increaseWindow command in kcftools is used to aggregate adjacent windows in a .kcf file into larger non-overlapping windows of a specified size. This operation can help smooth the signal, reduce noise, or adapt the resolution of KCF-based variation or similarity analyses to broader genomic scales.
Usage¶
$ kcftools increaseWindow -i=<inFile> -o=<outFile> -w=<windowSize>
Description¶
KCF files often contain fine-scale data, typically with window sizes like 100 bp or 1 kb. However, certain analyses—such as population-level statistics, whole-chromosome summaries, or broad variation scans—require coarser resolution.
This command merges consecutive windows to form larger, aggregated windows of the user-specified size. For example, if the original KCF file uses 1,000 bp windows, and --window 5000 is specified, every 5 adjacent windows (on the same chromosome) will be grouped into one.
During merging, attributes like variation scores, IBS values, and k-mer counts are aggregated, typically by recomputing, depending on the attribute type.
Options¶
| Option | Description | Required |
|---|---|---|
-i, --input=<inFile> |
Input .kcf file to process |
Yes |
-o, --output=<outFile> |
Output KCF file with merged windows | Yes |
-w, --window=<windowSize> |
Desired new window size (in base pairs) | Yes |
Output¶
The output is a .kcf file containing fewer but larger windows. Each new window is a merged region that summarizes attributes from its constituent smaller windows.
Example¶
$ kcftools increaseWindow -i genome_1kb.kcf -o genome_10kb.kcf -w 10000
This merges the original 1,000 bp windows into 10,000 bp windows, reducing granularity and improving interpretability at broader scales.
Note
- Windows are merged only if they are contiguous and on the same chromosome.
- The final window may be smaller if the chromosome length is not a perfect multiple of the new window size.
- This operation is ideal after variation detection (e.g., from
getVariations) and before matrix conversion (kcfToMatrix) when coarser analysis is desired.
Help¶
To view command-line help:
$ kcftools increaseWindow --help