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Improve flexibility of Genotype Matrix and Flat-file formats #10

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carolyncaron opened this issue Apr 28, 2017 · 0 comments
Open

Improve flexibility of Genotype Matrix and Flat-file formats #10

carolyncaron opened this issue Apr 28, 2017 · 0 comments
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@carolyncaron
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carolyncaron commented Apr 28, 2017

The current suggested formats are too restrictive.

Suggested Flat-file format:

  1. Variant name (required)
  2. Marker name (optional)
  3. Chromosome (required, unless select only)
  4. Position (required, unless select only)
  5. Sample name (required)
  6. Genotype Call (required)
  7. Meta-data (optional) (refer to issue Assign quality metrics to each genotype as they are loaded #5 for suggested format)

Suggested Matrix format:

  1. Variant name (required)
  2. Marker name (optional)
  3. Chromosome (required, unless select only)
  4. Position (required, unless select only)
  5. Genotype call (required) PLUS meta-data* (optional)

*Also see issue #5 for more context regarding how we propose to handle meta-data

Not sure whether this should be in its own issue, but it has also been discussed that users can suggest a custom format for marker name through the use of tokens with chromosome + position.

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