Overview

Summary of available tools.

GAMtools provides a number of different utilities for working with GAM data. The table below summarizes the tools available in the suite.

Utility	Description
bias	Calculate possible biases for a given genomic feature
call_windows	Call positive windows for individual NPs
compaction	Calculate chromatin compaction
convert	Convert between different GAM matrix formats
enrichment	Calculate enrichments of SLICE interactions
matrix	Generate a GAM matrix from a segregation file
permute_segregation	Circularly permute the columns of a GAM segregation file
process_nps	Map raw GAM sequencing data and call positive windows
radial_pos	Calculate chromatin radial position
resolution_qc	Calculate QC parameters for a segregation file
select	Select only certain samples from a segregation file