How can we know that the alignment files (bam) contains error alignment?

Question

[Calvin]

Hi, all Part of my project is to compare each alignment tools with different parameter. So i am wondering if there was any tool could verify bam files wether their alignment is correct or not?

[Medhat]

take a look at this https://sourceforge.net/projects/arden/

ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation

Answer 1

[Calvin]

Sorry, the error alignment means the percentage of reads mapped while violating the mapping criteria.

Answer 2

[kdjteda]

try samtools flagstat