Pairwise clustering by SNV sets

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.

Inputs

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.

Outputs

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)