I need to compare the performance of 2 or more alignment software (e.g. BWA, a new software X) while aligning a particular gene (e.g. HLA-A) against hg19 as human reference genome. Basically, i need to know sensitivity, Specificity, Accuracy, False Positive, False Negative of these software taking the same set of gene as input and against same reference human genome. Although BWA gives basic alignment summary and we can have a overall look via evaluating mapping file (.bam) using IGV but is there any other better way to look the overall alignment summary by different software of same genomic region of human genome after mapping by different software for their performance comparison ?. Looking for suggestions, Many thanks.