Nick Watts
Nick Watts
Separate "uncertain significance" from "conflicting interpretations of pathogenicity" and "conflicting data from submitters" in ClinVar track categories. https://atgu.slack.com/archives/CNLMF0JLV/p1614977312053800?thread_ts=1614722609.026400&cid=CNLMF0JLV
gnomAD v3.1 has two versions of quality metrics histograms: one raw and one with low quality genotypes filtered out. Currently, only the latter is displayed in the browser. Field names...
Demo deployments get very little traffic.
The GENCODE GTF files associated with gnomAD annotations are occasionally useful. For example, they are needed to get the gene and transcript version numbers for VEP annotations for Ensembl transcripts....
#371 started checking most Pylint warnings in PR checks. However, some warnings were left ignored because they occurred in existing code. Ignored warnings are listed in [`.pylintrc`](https://github.com/broadinstitute/gnomad_methods/blob/master/.pylintrc).
Some feedback on our current documentation: https://hail.zulipchat.com/#narrow/stream/123000-general/topic/Using.20Hail.20to.20download.20gnomAD.20data
Currently, we publish documentation on every commit to master, so https://broadinstitute.github.io/gnomad_methods/ contains documentation for the latest development version. However, users are likely using the last PyPI release, which may lag...
`slack_notifications` uses the process name from `sys.argv` in notifications. https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/utils/slack.py#L156-L172 However, someone may want notifications about multiple blocks in the same script. There should be a way to distinguish those...
* [ ] constraint * [ ] pext * [ ] MNVs Create resource modules to load these in the same way we read in public resources (e.g., `public_resource.ht()`)