exercise 1

tobiasrausch · Nov 29, 2024 · 89abb52 · 89abb52
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diff --git a/courses/cg/index.html b/courses/cg/index.html
@@ -15,9 +15,21 @@ <h3>Course Content</h3>
     <h3>Schedule</h3>
 
     <ul>
-      <li>Friday 22th November, 12:20pm-2pm: Lecture1 - Introduction to Cancer Genomics (Zoom), <a href="https://gear-genomics.embl.de/data/.slides/Lecture1_CancerGenomics.pdf">Slides</a></li>
+      <li>Friday 22th November, 12:20pm-2pm: Lecture1 - Introduction to Cancer Genomics (Zoom, Part1), <a href="https://gear-genomics.embl.de/data/.slides/Lecture1_CancerGenomics.pdf">Slides</a></li>
+      <li>Friday 29th November, 12:20pm-2pm: Lecture2 - Introduction to Cancer Genomics (Zoom, Part2), <a href="https://gear-genomics.embl.de/data/.slides/Lecture1_CancerGenomics.pdf">Slides</a></li>
     </ul>
 
+    <h3>Exercise 1: Variant Calling</h3>
+
+    The goal of this exercise is to create a simple variant calling workflow for human sequencing data of a simulated rare disease case. The workflow should contain steps to align the FASTQ files to the human reference genome (<a href="https://github.com/lh3/bwa">bwa</a>), call variants (<a href="https://samtools.github.io/bcftools/howtos/variant-calling.html">bcftools</a>) and annotate all single-nucleotide variants with (<a href="https://www.ensembl.org/Tools/VEP">VEP</a>). For this excercise you can ignore all short insertions and deletions and also structural variants. We are only interested in single-nucleotide variants (SNVs).Once you have finished the exercise, please send me the identified pathogenic variant using this <a href="https://forms.gle/B3azUnBxLJ4tFXN6A">google form</a> and don't forget to provide your email address that you used to register for the course.
+
+    <ul>
+      <li>Chromosome 7 human reference, <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr7.fa.gz">chr7</a></li>
+      <li>FASTQ of read1, <a href="https://gear-genomics.embl.de/data/.slides/R1.fastq.gz">Read1</a></li>
+      <li>FASTQ of read2, <a href="https://gear-genomics.embl.de/data/.slides/R2.fastq.gz">Read2</a></li>
+    </ul>
+
+
     <h3>Useful links</h3>
 
     Below are a couple of links to commonly used Bioinformatics tools in population and cancer genomics (certainly not comprehensive).