Say I use ART to simulate some short reads with the purpose of evaluating the performance of a mapper like bowtie or bwa. There is an option that will allow me to obtain a SAM file with the correct alignments.
Now let's say that I run an mapper and obtain a SAM file with its mappings.
So now I have two SAM files. One with the correct mappings and one with the mappings as determined by the mapper.
My question is, does anybody know of a script or program that will compare the two SAM files and output a report of the sensitivity and PPV?