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Update manipulating_vcf.md
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Netzach authored Aug 22, 2024
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Expand Up @@ -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)
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