The gamtools convert tool is used to convert proximity matrices output by GAMtools to/from various different formats.

Usage and option summary



Optional parameters:

Option Description
-i, –input-format Input matrix file format
-o, –output-format Output matrix file format
-t, –thresholds-file Thresholds file. If specified, any values lower than the specified thresholds will be masked/excluded from the output file
-w, –windows-file File containing the genomic locations of matrix bins (only required if not specified in input matrix file).
-r, –region Region covered by the input matrix (required if -w /–windows-file is specified)