BWA mapping quality scores?

[kweber2]

Thank you very much! -Kris

[nilshomer]

Does anyone know if BWA gives ambiguous reads a mapping quality score of 0? I believe I have read somewhere that it does, but I can't find this anywhere in the BWA documentation. (Actually, the only documentation I've found for BWA are the man page and the FAQ page. Is there more somewhere?) The FAQ page does mention that for paired-end reads, one read may have a mapping quality of 0 if it is ambiguous, and the other end can be non-zero. But are all ambiguous reads assigned a mapping quality of 0? Thanks!

That is correct. If a read maps to two or more places with equal score it is given a mapping quality of zero. Depending on the input options, it will output a random mapping or all mappings.

[kweber2]

Does anyone know if BWA gives ambiguous reads a mapping quality score of 0? I believe I have read somewhere that it does, but I can't find this anywhere in the BWA documentation. (Actually, the only documentation I've found for BWA are the man page and the FAQ page. Is there more somewhere?) The FAQ page does mention that for paired-end reads, one read may have a mapping quality of 0 if it is ambiguous, and the other end can be non-zero. But are all ambiguous reads assigned a mapping quality of 0? Thanks!