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Easier specification of build 38/build 37 sites #44

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chapmanb
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Thanks so much for adding the build 38 sites and support. I've been testing this and wanted to push a small fix to make it easier to specify build 37 or 38; this allows peddy to look these up from the internal library. It would be awesome to have this out as a release as well so we can start using it. Thanks again for making 38 support happen.

Allows users to specify 'GRCH37.sites' or 'GRCH38.sites' to swap
between build 37 and 38 without needing to know the internal
peddy path where installed.

Allows users to specify 'GRCH37.sites' or 'GRCH38.sites' to swap
between build 37 and 38 without needing to know the internal
peddy path where installed.
@brentp
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brentp commented May 30, 2018

Hi Brad, I'm working out some kinks of the hg38 stuff in a branch that will allow --sites hg38 which will automatically use the installed one. I'll make a new release once I have a chance to fix all that up. I think that will be next week.

@chapmanb
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Brent;
Thanks, sorry for pushing so much, we just have some hg38 projects that peddy would be useful for so have been working with the latest GitHub version to make happen. Let me know if there is anything I can do to help.

@brentp
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brentp commented May 30, 2018

Hi Brad, I have just tagged and set v0.4.1 to pypi.
It allows the user to specify --sites hg38 and it will find the appropriate set included with the distribution. please give it a try and let me know any issues.

@brentp brentp closed this May 30, 2018
chapmanb added a commit to bcbio/bcbio-nextgen that referenced this pull request Jun 1, 2018
- Adds support for hg38 with peddy. brentp/peddy#44
- Capture low overlap failures during PCA analysis, skipping peddy run
- Avoids using ensemble inputs for peddy, instead preferring single caller
  outputs. #2384
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2 participants