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Update 07_variant_calling.md
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epartan authored May 29, 2024
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Expand Up @@ -327,13 +327,13 @@ Instead, we will use the figure below taken from the [TCGA VCF 1.1 Specification
A VCF file is composed of **three main parts**:

### 1. Header
This contains meta-information Lines that provide supplemental information and they always **start with `##`**
This contains meta-information lines that provide supplemental information and they always **start with `##`**
* Lines can be applicable to all variant records in the file (e.g., date of creation of file) OR
* Lines can be specific to individual variants (e.g. flag to indicate whether a given variant exists in dbSNP)

### 2a. Fixed Fields

A line **starting with a single `#`** and contains headers for all columns in the Body of the file. The following **eight mandatory fields** will be found in every VCF file:
A line **starting with a single `#`** that contains headers for all columns in the Body of the file. The following **eight mandatory fields** will be found in every VCF file:

- **CHROM** - Chromosome where the variant was found
- **POS** - A 1-based index for the position on the chromosome where the variant was found. For multibase variants, this corresponds to the first base's position.
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**Exercise**

First let's move into out `variant_calling` directory and copy over a sample VCF file:
First let's move into our `variant_calling` directory and copy over a sample VCF file:

``` bash
cd ~/variant_calling/
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