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[WIP] User Story PBS #9

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daletovar opened this issue Jul 22, 2020 · 1 comment
Open

[WIP] User Story PBS #9

daletovar opened this issue Jul 22, 2020 · 1 comment

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@daletovar
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After doing some initial data preparation steps, PBS consists of doing:

  1. an allele count for each population.
    • sgkit.count_alleles will do this.
  2. locate and subset to segregating variants at sufficient frequency.
    -requires an is_biallelic_01 function.
    -requires a to_frequencies function, or some equivalent operation.
  3. setup windows over the genome.
    -requires a moving_statistic function.
  4. calculate the PBS in a moving window.
    -requires a pbs function.

Here is the notebook that @alimanfoo made.

@jerowe
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jerowe commented Jul 23, 2020

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