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💥 define a SMARTER snp coordinate version #37

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bunop opened this issue Nov 11, 2021 · 0 comments
Open
1 of 4 tasks

💥 define a SMARTER snp coordinate version #37

bunop opened this issue Nov 11, 2021 · 0 comments
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enhancement New feature or request performance Improve the performance or better resource management
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@bunop
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bunop commented Nov 11, 2021

Is your feature request related to a problem? Please describe.
Variant information comes from different sources, each one describing only a subset of all smarter variants. The SMARTER coordinate version should merge the most updated and trusted information and provide a final set of coordinates used to generate the most updated genotype file

Describe the solution you'd like
A solution could be trying to align probes directly to the genome of interest. This could solve ambiguities, determine new relations between chips and get information on the latest assembly

Describe alternatives you've considered
All the evidences for a variation should be compared and order by updated times and by autority. The most updated and trusted coordinates should be used to define a smarter coordinate source which can be displayed in API and web interface.

Additional context

  • track dates when importing snps from snpchimp
  • illumina_top attribute should be checked during insertion and written in to database
  • merge and rank evidences
  • define a comprehensive coordinate version relying on different evidences
@bunop bunop added enhancement New feature or request performance Improve the performance or better resource management labels Nov 11, 2021
@bunop bunop added this to the SMARTER database v1.0.0 milestone Nov 11, 2021
@bunop bunop added this to To do in SMARTER via automation Nov 11, 2021
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Labels
enhancement New feature or request performance Improve the performance or better resource management
Projects
Status: To do
SMARTER
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