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typo pt-4-map-call.md
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srisarya authored Sep 30, 2024
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## 4. Variant calling

Create a new directory in your `home` for the second part of today's practical
(e.g., `2024-09-02-genotyping`). You will want to set up the relevant
(e.g., `2024-09-30-genotyping`). You will want to set up the relevant
subdirectories and `WHATIDID.txt` file, as you have done before. Then symlink (`ln -s`) the
reference genome `/shared/data/popgen/reference.fa` and the alignments
from the mapping part of the practical (both `.bam` and `.bai` files) to your
`input` directory.

> **_Note:_**
> When you create links from one directory to another, it is better to use the absolute path for links like `~/2024-09-02-mapping/results/*.bam*` instead of `../../2024-09-30-mapping/results/*.bam`
> When you create links from one directory to another, it is better to use the absolute path for links like `~/2024-09-30-mapping/results/*.bam*` instead of `../../2024-09-30-mapping/results/*.bam`
> **_Note:_**
> Remember to keep your commands in the `WHATIDID.txt` file.
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