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Add I_n (informativeness for assignment) to marker table#56

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standage merged 4 commits intomasterfrom
informativeness
Feb 13, 2020
Merged

Add I_n (informativeness for assignment) to marker table#56
standage merged 4 commits intomasterfrom
informativeness

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This update uses Noah Rosenberg's infocalc script for calculating In for each marker from 1000 Genomes Project Phase 3 genotypes. This provides another criterion (in addition to AvgAe) for ranking markers for different forensic purposes.

@standage standage added enhancement New feature or request datasources References to existing data sources or proposals for new sources labels Feb 13, 2020
@standage standage merged commit d61f433 into master Feb 13, 2020
@standage standage deleted the informativeness branch February 13, 2020 19:33
standage pushed a commit that referenced this pull request Sep 11, 2024
Previously the `usa` panel included 100 loci for which there was *supposed* to be allele frequency data for all 19 sub-populations in a mock population roughly matching demographics in the United States. Due to a bug in that code, some loci in the panel do not have allele frequency data available for all populations. Also, since the initial panel slated for evaluation on real data (`beta`) contains 50 loci, it makes sense to restrict the `usa` panel to 50 loci as well.

This update fixes the bug and limits the panel to the top 50 loci ranked by A<sub>e</sub>.

Related to #55.
standage pushed a commit that referenced this pull request Sep 11, 2024
This update includes the results from a recent re-run of the USA8k Snakemake workflow, with the following changes.

- 150k reads simulated per sample rather than 250k reads
- new 50-microhap USA panel (see #56)
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