ngs plot

Overview

The ngs plot utility is an experimental subcommand that facilitates the creation of plots for data produced by ngs qc. Underneath the hood, all of the plots are generated by the excellent plotly library. Both sample-level (individual) and cohort-level (multiple samples) are supported, though not necessarily for the same set of graphs.

Sample-level graphs

The following sample level graphs are generated when one calls ngs plot sample:

Graph name	Description
GC Content Distribution	A graph showing the detected distribution of GC content for records contained within the file for one sample.
Quality Scores Distribution	A visualization showing the the first, second (median), and third quartiles of quality scores by position in the record

Cohort-level graphs

The following sample level graphs are generated when one calls ngs plot cohort:

Graph name	Description
GC Content Distribution	A graph showing the detected distribution of GC content for records contained within all specified files.