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BenLangmead / qtip

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
MIT License
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Implement aligner modifications upstream? #1

Closed johanneskoester closed 7 years ago

johanneskoester commented 7 years ago

Dear Ben, are there any plans or efforts to push the aligner modifications to upstream? I want to put qtip into Bioconda, but for that, it would be desirable to be able to depend on vanilla aligner packages.

Best, Johannes

johanneskoester commented 7 years ago

Am I right that bowtie2 2.3.0 already works out of the box?

johanneskoester commented 7 years ago

@BenLangmead any update on this?

BenLangmead commented 7 years ago

Sorry for the delay! Yes, the Bowtie 2 aligner modifications have been in releases starting with 2.3.1 (I think? I'll double-check, but I'm confident they're in the latest version.) qtip automatically specifies the --mapq-extra option when running Bowtie 2, which activates the appropriate feature output.

BenLangmead commented 7 years ago

v2.3.2 was the first release that had the exact kind of output used in the paper. It hasn't changed since then. (The --mapq-extra may also work in prior versions, but it very likely won't give the full set of features used in the paper.)

johanneskoester commented 7 years ago

Thanks! What about BWA? Is there a PR already?

BenLangmead commented 7 years ago

I just made a BWA MEM PR: https://github.com/lh3/bwa/pull/156

johanneskoester commented 7 years ago

Great, thank you!