bwa misalignment for TruSeq Amplicon reads

Question

[idedios]

I'm having the following issues using bwa mem on paired-end TruSeq Amplicon reads. I used the default settings with mem. The top sequence is from bwa mem. The bottom is from Illumina's BaseSpace analysis.

Answer 1

[idedios]

Any comments?

[karl.stamm]

You didn't ask a question. This isn't an answer. Biostars isn't a forum, it's Q&A, so these posts should be answers to questions. You didn't have a question in the original post.

I guess you don't like that the top part of the image has red and blue colored reads? See how the Illumina basespace has shorter reads? They have been trimmed, which will impact alignment.

[idedios]

Thanks this was the answer I was looking for.

I didn't know why bwa was doing what it was or how Illumina made their reads look the way they did. All I knew was that because of my "un-trimmed" reads vardict was calling a lot of false indels.

[idedios]

So the next question is what did Illumina trim from their reads to make it look the way they did? Usually the only trim settings I come by are trimming the adapters but that's definitely not the case here. I have a .bed file with the regions each amplicon should cover.

Is there a way to trim the reads in the bam file so that only what is covered in the bed reference file is kept?