bwa MEM for illumina 1.3+

Question

[Zev.Kronenberg]

I see that BWA ALN has an -I flag for changing the quality of the reads. I don't see this option for BWA MEM? Does anyone know if I'm missing something?

[Devon Ryan]

You're not missing anything: Bwa Mem: How To Specify The Fastq Phred Format? (see my link to a bwa email list message about this from Heng Li).

[Pierre Lindenbaum]

What is the size of your reads ? See Heng's comment:Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem

BWA-MEM however lacks the following features:

• Working with very short reads. The performance and the accuracy of BWA-MEM will degrade.
• Guaranteed sensitivity to hits within a certain edit distance threshold (as with BWA and GEM).

[Zev.Kronenberg]

100bp. I wanted to use mem for consistency across some simulations and real data.

[Adrian Pelin]

Honestly, I was stuck between mem and aln for my 100bp data, and aln performed much better, more reads aligned.

Answer 1

[Brian Bushnell]

You can use my reformat tool to change ASCII-64 qualities to ASCII-33 (and most other format conversions). It supports piping from stdin and to stdout, so you don't have to write a temp file. And it's the fastest format convert of which I am aware.