Evaluating Mappings

• Overview
• Key Options
• Output

Overview

The dwgsim_eval tool evaluates the mappings from reads produced by dwgsim. See the dwgsim tool for Simulating Reads.

Use dwgsim_eval -h to see the full set of command line options (usage).

An example command is as follows:

dwgsim_eval mapped.bam

A read is correctly mapped if the mapped start position is within INT bases (-g) of the simulated read's start position. Otherwise, it is counted as incorrectly mapped. Furthermore, random reads created by dwgsim are expected to be unmapped (counted as false mappings otherwise).

Key Options

• Use the -c option if the reads are from SOLID
• Use the -b option if the alignments are from BWA when mapping SOLiD reads
• Use the -z option if the input reads are expected to be single end (not paired end)
• Use the -s option if the input is a SAM file (default: BAM)
• Use the -n option to specify the number of reads if only a subset of the input reads were used (affects the denominator)

Output

The dwgsim_eval tool outputs a table with the following columns:

Column	Description
thr	The alignment threshold (see -a)
mc	The number of reads mapped correctly that should be mapped at the threshold
mi	The number of reads mapped incorrectly that should be mapped be mapped at the threshold
mu	The number of reads unmapped that should be mapped be mapped at the threshold
um	The number of reads mapped that should be unmapped be mapped at the threshold
uu	The number of reads unmapped that should be unmapped be mapped at the threshold
mc + mi + mu + um + uu	The total number of reads that should be unmapped be mapped at the threshold
mc'	The number of reads mapped correctly that should be mapped at or greater than the threshold
mi'	The number of reads mapped incorrectly that should be mapped be mapped at or greater than the threshold
mu'	The number of reads unmapped that should be mapped be mapped at or greater than the threshold
um'	The number of reads mapped that should be unmapped be mapped at or greater than the threshold
uu'	The number of reads unmapped that should be unmapped be mapped at or greater than the threshold
mc' + mi' + mu' + um' + uu'	The total number of reads that should be unmapped be mapped at or greater than the threshold
mc / (mc + mi + mu)	Sensitivity at the threshold. I.e. the fraction of reads that should be mapped that are mapped correctly.
mc / (mc + mi)	Positive predictive value at the threshold. I.e. The fraction of mapped reads that are mapped correctly.
um / (um + uu)	False discovery rate at the threshold. I.e. The fraction of random reads that are mapped.
mc' / (mc' + mi' + mu')	Sensitivity at or greater than the threshold. I.e. the fraction of reads that should be mapped that are mapped correctly.
mc' / (mc' + mi')	Positive predictive value at or greater than the threshold. I.e. The fraction of mapped reads that are mapped correctly.
um' / (um' + uu')	False discovery rate at or greater than the threshold. I.e. The fraction of random reads that are mapped.

"At or greater than the threshold" tells us what our sensitivity, PPV, and FDR would be if we filtered based on that threshold.