mapping quality for sanger reads

Question

[shinken123]

Hi

Anyone knows if BWA-mem automatically detect if the reads that I am aligning have their quality is fastq-sanger?. If not, this affect the mapping quality score?

Cheers

Answer 1

[Ashutosh Pandey]

BWA aln provides -I option that can be used to align fastq reads with Phred+64 quality scores. The reads in output bam file have base quality in Sanger or Phred+33 format. BWA-mem doesn't have that option (at least not stated in the manual). If you search on this forum there are multiple posts that explain in detail about how to test if reads belong to Phred+33 or Phred+64. Also, you can easily convert them from one to other. Base quality scores are not used in the calculation of mapping quality scores but BWA mem may throw an out of range error if it can't take Phred+64 fastq files.

[shinken123]

Thank you very much. So if my reads are from a sanger sequencing (Phred+33) and BWA-mem assumes that the sequences are in Phred+33, is going to work fine with my data.

Thanks again

Regards

[Ashutosh Pandey]

Well if your reads are phred+33 then you don't need to do anything. Just use BWA mem.