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5.7 years ago
grant.hovhannisyan
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2.6k
Do/How do Phred quality scores influence the read mapping? Can you share any software documentation describing that?
I think most programs ignore read quality (but I don't have data to back my claim). There is an old thread (with links) stating BWA doesn't use base qualities ( does bwa mem use base qualities? ). The original information is here:
https://github.com/lh3/mem-paper/blob/master/response_to_aaron.md
Thanks! A bit surprising to be honest, one would expect lower probability to map if you are not sure about the nucleotide.
Bowtie2 seems to use read quality, although the manual is not entirely clear on how:
I am basically planning to simulate and map reads and was wondering whether the ability to simulate quality scores is important when choosing simulation software.