chapmanb/bcbb — Issue #47: bwa quality values
Author: percyfal
Created: 2011-12-09 09:50:32+00:00
State: open

Hi Brad!

I've been using bcbb for exome analysis and have used bwa as the aligner. We have illumina data, so quality_format: Illumina in post_process.yaml. However, as far as I can see, ngsalign/bwa.py doesn't use this information. From bwa aln:

bwa aln

-I the input is in the Illumina 1.3+ FASTQ-like format

However, I ran some tests on bwa (0.5.9-r16) with and without the flag, which gave the same mapping results (qualities etc), so I'm wondering if you left this out on purpose? It would seem bwa makes a guess about the quality format, after all?

Cheers,

Per