Answers.Body: <p>Based on the way you've called the command (using <code>-xl-sn</code>), I assume you are using GATK 4 and not GATK 3.</p>
  
  <p>If this is the case, the documentation for the <code>-xl-sn</code> flag is available here: <a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_variantutils_SelectVariants.php#--exclude-sample-name" rel="nofollow noreferrer">https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_variantutils_SelectVariants.php#--exclude-sample-name</a>.</p>
  
  <p>By default, the <code>-xl-sn SAMPLE</code> means "exclude the sample called SAMPLE from my VCF". In your case, you're providing an entire list of samples, in a file, which is not the default behaviour. In order to tell GATK that you're providing a file and not a sample name, <strong>you need to ensure the file you provide has the extension <code>.args</code></strong>.</p>
  
  <p>From the documentation:</p>
  
  <blockquote>
    <p>File names must use the extension ".args"</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-30T13:46:41.787Z
Answers.Text: ok cool it worked thanks mate (Y)
Answers.UserDisplayName: Syed M. Ijlal Haider
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-30T13:24:35.680Z
Answers.LastActivityDate: 2019-07-30T13:24:35.680Z
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Body: <p>I need some help with GATK. I have a multisample vcf file containing 18125 samples. After performing PCA I have around 303 samples as outliers and I wanted to remove these samples from my multisample vcf file.</p>
  
  <p>I tried doing it using the GATK <code>SelectVariant</code> tool. It does some stuff and generates a VCF file which is a bit smaller in size than the original file, but in the end the total count of samples remains the same. As I have no prior knowledge of GATK (working with it for the first time) I am just wondering if you guys can help me out in fixing this issue. </p>
  
  <p>The command that I used was </p>
  
  <pre><code>gatk SelectVariants -V filtered.vcf -xl-sn remove.txt -O test.vcf 
  </code></pre>
  
  <p><code>remove.txt</code> contains the sample names in each row (1 sample per row).</p>
  
  <p>After running this command it generated a <code>test.vcf</code> file, for which I counted samples using:</p>
  
  <pre><code>bcftools query -l test.vcf | wc -l
  </code></pre>
  
  <p>However, I got exactly same number of samples as in the original VCF file <code>filtered.vcf</code>.</p>
  
Tags: <vcf><quality-control><gatk>
Title: Subset a multisample VCF file
ThreadText: # Subset a multisample VCF file
  
  (Asked by: username_0 on 2019-07-30)
  
  I need some help with GATK. I have a multisample vcf file containing 18125 samples. After performing PCA I have around 303 samples as outliers and I wanted to remove these samples from my multisample vcf file.
  
  I tried doing it using the GATK `SelectVariant` tool. It does some stuff and generates a VCF file which is a bit smaller in size than the original file, but in the end the total count of samples remains the same. As I have no prior knowledge of GATK (working with it for the first time) I am just wondering if you guys can help me out in fixing this issue.
  
  The command that I used was
  
  ```
  gatk SelectVariants -V filtered.vcf -xl-sn remove.txt -O test.vcf 
  
  ```
  
  `remove.txt` contains the sample names in each row (1 sample per row).
  
  After running this command it generated a `test.vcf` file, for which I counted samples using:
  
  ```
  bcftools query -l test.vcf | wc -l
  
  ```
  
  However, I got exactly same number of samples as in the original VCF file `filtered.vcf`.
  
  **Tags:** vcf, quality-control, gatk
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-07-30. Score: 3 | Accepted answer
  
  Based on the way you've called the command (using `-xl-sn`), I assume you are using GATK 4 and not GATK 3.
  
  If this is the case, the documentation for the `-xl-sn` flag is available here: <https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_variantutils_SelectVariants.php#--exclude-sample-name>.
  
  By default, the `-xl-sn SAMPLE` means "exclude the sample called SAMPLE from my VCF". In your case, you're providing an entire list of samples, in a file, which is not the default behaviour. In order to tell GATK that you're providing a file and not a sample name, **you need to ensure the file you provide has the extension `.args`**.
  
  From the documentation:
  
  > File names must use the extension ".args"
  
  > **Comments:**
  > **username_0**: ok cool it worked thanks mate (Y)  
  
  ---
  
  