cg 2024

courses/cg/index.html

@@ -28,7 +28,7 @@ <h3>Schedule</h3>
 
     <h3>Exercise 1: Variant Calling (due date 24th April 2024)</h3>
 
-    Please create a GitHub account or login to your existing account and create a new repository to analyse sequencing data. The goal of this exercise is to create a simple variant calling workflow for human sequencing data. Please describe the steps of your workflow using markdown (<a href="https://docs.github.com/en/get-started/writing-on-github">GitHub Markdown</a>). 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 variants (<a href="https://www.ensembl.org/Tools/VEP">VEP</a>). Once you have finished the exercise, send me the repository URL of your GitHub repository and the likely causative variant via email.
+    Please create a GitHub account or login to your existing account and create a new repository to analyse sequencing data. The goal of this exercise is to create a simple variant calling workflow for human sequencing data. Please describe the steps of your workflow using markdown (<a href="https://docs.github.com/en/get-started/writing-on-github">GitHub Markdown</a>). 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 InDels. Once you have finished the exercise, send me the repository URL of your GitHub repository and the likely causative variant via email.
 
     <ul>
       <li>Chromosome 7 human reference, <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr7.fa.gz">chr7</a></li>