Ngsrich Output Explanation

Question

[mark.dunning]

I am trying to use the NGSrich tool to compute and visualise enrichment of target regions in an exome-sequencing experiment.

http://sourceforge.net/projects/ngsrich/

The tool seems to produce some useful output to hand to my collaborators, but I am not clear on the metrics reported in the HTML file. Does anyone have any detailed explanation of these metrics? Specifically,

The #target regions metric seems to differ if I gave the same target regions file, but different bam files

Do the Coverage metrics refer to On-target reads only? And on a per-base or per-Amplicon basis? What exactly are the percentage reported?

Regards,

Mark

[Jeremy Leipzig]

is there an example of the output somewhere?

[Sean Davis]

Have you tried asking the authors? The package does not seem to have documentation that includes that level of detail.

Answer 1

[mark.dunning]

Here is an example of the stats produced on the HTML page. I feel that some explanation would be useful

[Jeremy Leipzig]

i speculate the covered metrics are almost certainly the fraction of the regions of interest covered at varying depths. "Covered 1x" makes no sense otherwise (how could on-target+off-target be anything but 100%)