Update manipulating_vcf.md

docs/Case_studies/manipulating_vcf.md

@@ -71,14 +71,15 @@ A table with counted and sorted different genomic features in chromosome 4.
 Start by splitting the task into sub-tasks. This makes it easier to see what happens and you might get interesting intermediary results. 
 
 ??? "_Hint_, Example"
-Let's say we want to find out all genes that contains a variant and all variants that are located within a gene. What do we want to do first? Take a look at the vcf file. That is the one that contains all the variants. Then look at the gff file, which contains the genes and other annotations. Finally, take a look at the DNA sequence. You will need to combine all three to answer the question. 
-
+    ```Let's say we want to find out all genes that contains a variant and all variants that are located within a gene. What do we want to do first? Take a look at the vcf file. That is the one that contains all the variants. Then look at the gff file, which contains the genes and other annotations. Finally, take a look at the DNA sequence. You will need to combine all three to answer the question. 
+    ```
+    ```
 ??? "_Hint_, Example, what do we need to get?"
 * Positions for SNPs and INDELs
 * Positions for genes and CDSs
 * Separation of variants (SNPs and INDELs) into two groups, inside and outside genes (and CDSs)
 * Separation of genes/CDSs into those with and without variants (and maybe how many there are per gene)
-
+    ```
 ### The exercise
 Identify the steps you need to do and what each step does. Open the hints if you get stuck.