diff --git a/docs/Case_studies/manipulating_vcf.md b/docs/Case_studies/manipulating_vcf.md index 5003e49..ccdd14b 100644 --- a/docs/Case_studies/manipulating_vcf.md +++ b/docs/Case_studies/manipulating_vcf.md @@ -71,10 +71,11 @@ 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)