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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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bwa quality values #47

Closed percyfal closed 12 years ago

percyfal commented 12 years ago

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

chapmanb commented 12 years ago

Per; Thanks for this. bwa does a good job without the flag, but I'm agreed we should set it explicitly. I just checked in a fix:

https://github.com/chapmanb/bcbb/commit/cfbc3b097a2a3ca23dc835f147709b6ecf5d450d

Thanks again, Brad