Answers.Body: <p>The issue was that not installing the most recent version of Conda.
  It was solved by changing the .condarc file to <strong>solely</strong> include the following lines:</p>
  <pre><code>channels:
      - conda-forge
      - bioconda
      - defaults
  </code></pre>
  <p>The order is crucial as well.</p>
  <p><em>Converted to answer from question.</em></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-23T22:11:18.167Z
Answers.LastActivityDate: 2022-11-23T22:11:18.167Z
Answers.UserDisplayName: user438383
Body: <p>I tried adding the F_MISSING tag using bcftools 1.16. When I run this command:</p>
  <pre><code>bcftools +fill-tags input.vcf.gz -- -t 'F_MISSING' | bcftools view -i 'INFO/F_MISSING&lt;0.25' -Oz -o output.vcf.gz
  </code></pre>
  <p>I get the following error:</p>
  <pre><code>Error parsing &quot;--tags F_MISSING&quot;: the tag &quot;F_MISSING&quot; is not supported
  </code></pre>
  <p>This command runs fine using bcftools 1.15. However, version 1.15 gives complications with other packages I use in my snakefile. Do you maybe know alternatives for how to add F_MISSING using bcftls 1.16 (if possible)?</p>
  <p>When I type <code>bcftools +fill-tags --version</code>:</p>
  <p>bcftools 1.9 using htslib 1.9</p>
  <p>plugin at 1.9 using htslib 1.9</p>
  <p>##SOLUTION##</p>
  <p>Indeed the issue was that I was not installing the most recent version of Conda.
  I solved it by changing the .condarc file to <strong>solelely</strong> include the following lines:</p>
  <pre><code>channels:
      - conda-forge
      - bioconda
      - defaults
  </code></pre>
  <p>The order is crucial as well.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-21T14:32:36.723Z
Comments.Text: Wait, what is version 1.9? Aren't you using version 1.16?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-21T14:36:08.503Z
Comments.Text: I know, I am pretty confused by that myself. I installed bcftools in a newly created conda env using ```conda install -c bioconda bcftools``` as indicated on https://anaconda.org/bioconda/bcftools and conda says v1.16
Comments.UserDisplayName: ra23mik
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-21T14:38:58.770Z
Comments.Text: Conda might, but are you running the version installed in conda or the one on your system? Don't you need something like `conda run bcftools --version`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-21T14:41:59.107Z
Comments.Text: I ran the following:
  ```conda activate bcftools1.16 ``` and then  ```conda list --show-channel-urls```.
  
  Just to check again the version of bcftools: 
  
  ```# Name                    Version                   Build  Channel```
  ```bcftools                  1.9                  h68d8f2e_9    bioconda```
Comments.UserDisplayName: ra23mik
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-21T15:56:42.043Z
Comments.Text: Please put all of this into the question. I don't know much about conda, but it still looks like you're running the system-wide one. What's the output of `type -a bcftools` and, `type -a bcftools | grep -v aliased | grep -oP '/\S+' | while read c; do echo "=== $c ==="; $c --version; done`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-23T14:15:47.683Z
Comments.Text: I solved it, I added my solution to the question.
Comments.UserDisplayName: ra23mik
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-23T14:37:52.990Z
Comments.Text: Great! But please post your solution as an answer instead so the question can be marked as slved.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-24T12:31:29.400Z
Comments.Text: Thank you for doing it for me. Very new to stackoverflow as you might have guessed.
Comments.UserDisplayName: ra23mik
Tags: <bcftools>
Title: Bcftools 1.16 able to add F_MISSING tag?
ThreadText: # Bcftools 1.16 able to add F_MISSING tag?
  
  (Asked by: username_0 on 2022-11-21)
  
  I tried adding the F\_MISSING tag using bcftools 1.16. When I run this command:
  
  ```
  bcftools +fill-tags input.vcf.gz -- -t 'F_MISSING' | bcftools view -i 'INFO/F_MISSING<0.25' -Oz -o output.vcf.gz
  
  ```
  
  I get the following error:
  
  ```
  Error parsing "--tags F_MISSING": the tag "F_MISSING" is not supported
  
  ```
  
  This command runs fine using bcftools 1.15. However, version 1.15 gives complications with other packages I use in my snakefile. Do you maybe know alternatives for how to add F\_MISSING using bcftls 1.16 (if possible)?
  
  When I type `bcftools +fill-tags --version`:
  
  bcftools 1.9 using htslib 1.9
  
  plugin at 1.9 using htslib 1.9
  
  ##SOLUTION##
  
  Indeed the issue was that I was not installing the most recent version of Conda.
  I solved it by changing the .condarc file to **solelely** include the following lines:
  
  ```
  channels:
      - conda-forge
      - bioconda
      - defaults
  
  ```
  
  The order is crucial as well.
  
  **Tags:** bcftools
  
  > **Comments:**
  > **username_1**: Wait, what is version 1.9? Aren't you using version 1.16?  
  > **username_0**: I know, I am pretty confused by that myself. I installed bcftools in a newly created conda env using ```conda install -c bioconda bcftools``` as indicated on https://anaconda.org/bioconda/bcftools and conda says v1.16  
  > **username_1**: Conda might, but are you running the version installed in conda or the one on your system? Don't you need something like `conda run bcftools --version`?  
  > **username_0**: I ran the following: ```conda activate bcftools1.16 ``` and then  ```conda list --show-channel-urls```.  Just to check again the version of bcftools:   ```# Name                    Version                   Build  Channel``` ```bcftools                  1.9                  h68d8f2e_9    bioconda```  
  > **username_1**: Please put all of this into the question. I don't know much about conda, but it still looks like you're running the system-wide one. What's the output of `type -a bcftools` and, `type -a bcftools | grep -v aliased | grep -oP '/\S+' | while read c; do echo "=== $c ==="; $c --version; done`?  
  > **username_0**: I solved it, I added my solution to the question.  
  > **username_1**: Great! But please post your solution as an answer instead so the question can be marked as slved.  
  > **username_0**: Thank you for doing it for me. Very new to stackoverflow as you might have guessed.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-11-23. Score: 0 | Accepted answer
  
  The issue was that not installing the most recent version of Conda.
  It was solved by changing the .condarc file to **solely** include the following lines:
  
  ```
  channels:
      - conda-forge
      - bioconda
      - defaults
  
  ```
  
  The order is crucial as well.
  
  *Converted to answer from question.*
  
  
  ---
  
  