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

- + 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
-

20-Aug-2023

+

22-Aug-2023

@@ -8993,7 +8993,7 @@

Out of Af - + 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

-

+

Figure 1: Coverage distributions for three hypothetical samples along with the cumulative coverage for all samples.
@@ -8692,16 +8692,16 @@

Input data

ls -lLh [CY]*.chr21.bam
-
-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
+
-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.

@@ -8841,7 +8841,7 @@

Total coverage

-

+

(a) Genome coverage
@@ -8849,7 +8849,7 @@

Total coverage

-

+

(b) Cumulative genome coverage
@@ -8870,7 +8870,7 @@

Total coverage

-

+

(a) Genome coverage
@@ -9266,7 +9266,7 @@

Variant filtering

- + 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 @@