From 630f093857b44c4d3158ab0dd252dec0dacd5f6b Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Tue, 22 Aug 2023 23:03:44 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- about.html | 2 +- exercises/data.html | 4 +- exercises/data_filtering/index.html | 30 +- .../figure-html/fig-coverage-filters-1-1.svg | 6 +- exercises/demopy/index.html | 4 +- exercises/index.html | 36 +- exercises/ld_and_phasing/index.html | 2 +- exercises/ld_pruning/index.html | 2 +- index.html | 2 +- lectures/genetic_diversity/index.html | 2 +- references.html | 6 + search.json | 337 +++++----- sitemap.xml | 92 +-- slides/admixture/index.html | 2 +- slides/applications_selection/index.html | 2 +- slides/datageneration/index.html | 2 +- .../figure-revealjs/coverage-filters-1-1.svg | 12 +- .../figure-revealjs/coverage-filters-2-1.svg | 12 +- .../figure-revealjs/coverage-filters-3-1.svg | 12 +- .../figure-revealjs/coverage-filters-4-1.svg | 12 +- .../figure-revealjs/coverage-filters-5-1.svg | 12 +- .../figure-revealjs/coverage-filters-6-1.svg | 12 +- .../figure-revealjs/coverage-filters-7-1.svg | 12 +- .../coverage-filters-final-1.svg | 12 +- slides/demo/index.html | 54 +- slides/demography/index.html | 2 +- slides/direct_selection/index.html | 2 +- slides/foundations/index.html | 614 +++++++++++++----- .../fig-black-footed-ferret-1.png | Bin 61733 -> 61599 bytes .../figure-revealjs/fig-dominance-1.png | Bin 0 -> 165805 bytes .../fig-genetic-drift-N-10-1.gif | Bin 627451 -> 625014 bytes .../fig-genetic-drift-many-repetitions-1.png | Bin 431132 -> 433285 bytes .../figure-revealjs/fig-gillespie-2.4-1.png | Bin 76995 -> 77636 bytes .../figure-revealjs/fig-hwe-1000genomes-1.png | Bin 0 -> 610716 bytes .../fig-identity-by-state-and-descent-1.svg | 8 +- .../fig-selection-and-drift-1.png | Bin 0 -> 71406 bytes .../figure-revealjs/gas-particle-drift-1.svg | 67 ++ .../figure-revealjs/mutation-models-1.svg | 4 +- .../stepwise-mutation-model-1.svg | 10 +- slides/genetic_diversity/index.html | 2 +- slides/index.html | 36 +- slides/introduction/index.html | 2 +- slides/ld_and_recombination/index.html | 2 +- slides/linked_selection/index.html | 2 +- slides/pgip/index.html | 92 +-- slides/population_structure/index.html | 2 +- .../fst-independent-population-model-1.svg | 6 +- slides/recap_day1/index.html | 2 +- slides/recap_day2/index.html | 2 +- slides/recap_day3/index.html | 2 +- slides/recap_day4/index.html | 2 +- slides/simulation/index.html | 98 ++- .../fig-genealogy-properties-1.svg | 422 ++++++++++++ .../fig-simulate-genealogy-end-1.svg | 4 +- .../simulate-genealogy-1-1.svg | 4 +- .../simulate-genealogy-10-1.svg | 4 +- .../simulate-genealogy-11-1.svg | 4 +- .../simulate-genealogy-2-1.svg | 4 +- .../simulate-genealogy-3-1.svg | 4 +- .../simulate-genealogy-4-1.svg | 4 +- .../simulate-genealogy-5-1.svg | 4 +- .../simulate-genealogy-6-1.svg | 4 +- .../simulate-genealogy-7-1.svg | 4 +- .../simulate-genealogy-8-1.svg | 4 +- .../simulate-genealogy-9-1.svg | 4 +- 66 files changed, 1460 insertions(+), 650 deletions(-) create mode 100644 slides/foundations/index_files/figure-revealjs/fig-dominance-1.png create mode 100644 slides/foundations/index_files/figure-revealjs/fig-hwe-1000genomes-1.png create mode 100644 slides/foundations/index_files/figure-revealjs/fig-selection-and-drift-1.png create mode 100644 slides/foundations/index_files/figure-revealjs/gas-particle-drift-1.svg create mode 100644 slides/simulation/index_files/figure-revealjs/fig-genealogy-properties-1.svg diff --git a/.nojekyll b/.nojekyll index ed3c3871..eeb30041 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -c1bfc7bd \ No newline at end of file +270c34f1 \ No newline at end of file diff --git a/about.html b/about.html index d414999e..0880fbb2 100644 --- a/about.html +++ b/about.html @@ -8566,7 +8566,7 @@

NBIS

Published with Quarto v
- + diff --git a/exercises/data.html b/exercises/data.html index c4bb64c2..2f6e5e86 100644 --- a/exercises/data.html +++ b/exercises/data.html @@ -8599,7 +8599,7 @@

Data

Published
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20-Aug-2023

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22-Aug-2023

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Out of Af
Published with Quarto v
- + diff --git a/exercises/data_filtering/index.html b/exercises/data_filtering/index.html index 61200d9c..e8b94b6e 100644 --- a/exercises/data_filtering/index.html +++ b/exercises/data_filtering/index.html @@ -8645,7 +8645,7 @@

Filtering of resequencing data

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Figure 1: Coverage distributions for three hypothetical samples along with the cumulative coverage for all samples.
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Input data

ls -lLh [CY]*.chr21.bam
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-rw-r--r-- 1 runner docker 7.8M Aug 20 16:22 CEU-1.ooa.chr21.bam
--rw-r--r-- 1 runner docker 6.3M Aug 20 16:22 CEU-2.ooa.chr21.bam
--rw-r--r-- 1 runner docker 4.8M Aug 20 16:22 CEU-3.ooa.chr21.bam
--rw-r--r-- 1 runner docker  13M Aug 20 16:22 CEU-4.ooa.chr21.bam
--rw-r--r-- 1 runner docker 5.8M Aug 20 16:22 CHB-1.ooa.chr21.bam
--rw-r--r-- 1 runner docker 5.2M Aug 20 16:22 CHB-2.ooa.chr21.bam
--rw-r--r-- 1 runner docker 6.5M Aug 20 16:22 CHB-3.ooa.chr21.bam
--rw-r--r-- 1 runner docker 6.1M Aug 20 16:22 YRI-1.ooa.chr21.bam
--rw-r--r-- 1 runner docker 6.0M Aug 20 16:22 YRI-2.ooa.chr21.bam
--rw-r--r-- 1 runner docker 7.6M Aug 20 16:22 YRI-3.ooa.chr21.bam
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-rw-r--r-- 1 runner docker 7.8M Aug 22 22:55 CEU-1.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 6.3M Aug 22 22:55 CEU-2.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 4.8M Aug 22 22:55 CEU-3.ooa.chr21.bam
+-rw-r--r-- 1 runner docker  13M Aug 22 22:55 CEU-4.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 5.8M Aug 22 22:55 CHB-1.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 5.2M Aug 22 22:55 CHB-2.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 6.5M Aug 22 22:55 CHB-3.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 6.1M Aug 22 22:55 YRI-1.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 6.0M Aug 22 22:55 YRI-2.ooa.chr21.bam
+-rw-r--r-- 1 runner docker 7.6M Aug 22 22:55 YRI-3.ooa.chr21.bam

Each population consists of a collection – or set – of samples, and we will sometimes use the term sample set to refer to such a collection. For instance, the population (sample set) CHB consists of the set of samples CHB-1, CHB-2 and CHB-3.

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Total coverage

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(a) Genome coverage
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Total coverage

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(b) Cumulative genome coverage
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Total coverage

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(a) Genome coverage
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Variant filtering

Published with Quarto v
- + diff --git a/exercises/data_filtering/index_files/figure-html/fig-coverage-filters-1-1.svg b/exercises/data_filtering/index_files/figure-html/fig-coverage-filters-1-1.svg index 3a4df24d..ee684e6d 100644 --- a/exercises/data_filtering/index_files/figure-html/fig-coverage-filters-1-1.svg +++ b/exercises/data_filtering/index_files/figure-html/fig-coverage-filters-1-1.svg @@ -2,9 +2,9 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +drift + + + + + + + + + + + + +drift + + + + + + + + + \ No newline at end of file diff --git a/slides/foundations/index_files/figure-revealjs/mutation-models-1.svg b/slides/foundations/index_files/figure-revealjs/mutation-models-1.svg index a02396bc..4f8772c5 100644 --- a/slides/foundations/index_files/figure-revealjs/mutation-models-1.svg +++ b/slides/foundations/index_files/figure-revealjs/mutation-models-1.svg @@ -2,8 +2,8 @@