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

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?

alignment
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updated by kdjteda • kdjteda • written by Calvin • Calvin

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

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written by Medhat Medhat

2 answers

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

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written by Calvin • Calvin

try samtools flagstat

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written by kdjteda • kdjteda

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