I have aligned my reads against the reference genome using BWA, I removed the reads with low quality and deduplicated the alignment. How do I now that the results are correct?
Do I need to prove that the reads are mapped correctly by using a second aligner (which should confirm the results of BWA)? This approach I actually did not see it anywhere.
Essentially, I do I know that I am not using garbage? What is the consensus on quality control of the mapping?