calculating accuracy (false positives and false negatives) on Whole Genome Alignmen

Question

[joe_genome]

Hello,

I'm testing different alignment methods and see that in literature many times they use the accuracy of an alignment for a metric comparison, however, many times they don't actually mention how this was calculated. Is there a specific tool such as bedtools that is able to determine the accuracy of an alignment against a reference or is this done manually?

Thank you

[ATpoint]

Cannot help with the question at hand but there is extensive literature on benchmarking alignment and variant calling already. It is questionable to what extend your own testing will add to this, because after all you eventually will need to settle for a pipeline, and you can simply use one that has been accepted well in the literature rather than doing all that work over again.