Quick Start

This web application takes the results from VarSim SAMcompare and displays them in an interactive plot. For instructions on how to run SAMcompare, please see [link].

Steps for basic usage:

1. Run SAMcompare to generate one or more .json files that contains the accuracy results.
2. Click "Add data sets" (above) and select the .json files you would like to compare.
3. The resulting plots generated are grouped by the type of variation each read overlaps in the truth set.
4. You can click on the plots to change the selection mode.

Introduction

VarSim provides an easy and flexible way to compare secondary analysis workflows. Alignment Compare is for displaying the accuracy results for alignment tools based on the truth set generated by VarSim. It is able to break down the comparison into different regions of the genome based on the type of variant each read overlaps. The curves are generated by varying the MAPQ cut-off.

Details

Plot generation

The plots are generated by varying the MAPQ cut-off. That is for each point alignments are filtered as greater or equal to the MAPQ value.

Axes

VarSim plots Sensitivity (TPR) versus FDR. TPR is defined as TP/(TP+FN) and FDR is defined as FP/(FP+TP).

Selection modes

• Closest point: The closest (euclidian) point to the cursor for each series will be selected.
• X lock: The closest (euclidian) point to the cursor on the X-axis for each series will be selected.
• Y lock: The closest (euclidian) point to the cursor on the Y-axis for each series will be selected.
• Closest MAPQ: The MAPQ of the closest (euclidian) point to the cursor is recorded. For each series, the point with the closest MAPQ to this value is selected.

Limitations

Points with less than 30% of the reads aligned are not plotted since those are potentially noisy and not so useful.