This script takes a table of sample IDs and VCF file paths and outputs an SNV difference matrix and cluster assignments according to the SNV difference threshold defined by the user.
You can view options by running Rscript pairwiseclustering.r --help.
usage: pairwiseclustering.r [-h] -i IDS -f FRONTCLIP -b BACKCLIP [-o ODIR]
[-t THRESHOLD]
optional arguments:
-h, --help show this help message and exit
-i IDS, --ids IDS file with sample IDs
-f FRONTCLIP, --frontclip FRONTCLIP bases to clip from the front
-b BACKCLIP, --backclip BACKCLIP bases to clip from the back
-o ODIR, --odir ODIR output directory
-t THRESHOLD, --threshold THRESHOLD SNV difference threshold for clustering
| Flag | Description |
|---|---|
-i |
CSV file with two columns. The left column should contain sample IDs and the right column should contain paths to VCF files. |
-o |
Output directory. The default is $PWD. |
-f |
The number of nucleotides to clip from the front end of the reference sequence. |
-b |
The number of nucleotides to clip from the back end of the reference sequence. |
-t |
The SNV error threshold to use when assigning clusters. The default is 0 SNVs. |
The script outputs the difference matrix and cluster assignments into the output directory of your choice.
| Filename | Contents |
|---|---|
differences.csv |
Difference matrix. Rows and columns are in the same order. |
clusters.csv |
Table of samples IDs (left column) and numeric cluster IDs (right column) |