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:
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.
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.
VarSim plots Sensitivity (TPR) versus FDR. TPR is defined as TP/(TP+FN) and FDR is defined as FP/(FP+TP).
Points with less than 30% of the reads aligned are not plotted since those are potentially noisy and not so useful.