<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>

CC BY-SA 4.0
2022-11-23T22:11:18.167Z
2022-11-23T22:11:18.167Z
user438383
<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>

CC BY-SA 4.0
2022-11-21T14:32:36.723Z
Wait, what is version 1.9? Aren't you using version 1.16?
terdon
CC BY-SA 4.0
2022-11-21T14:36:08.503Z
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
ra23mik
CC BY-SA 4.0
2022-11-21T14:38:58.770Z
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`?
terdon
CC BY-SA 4.0
2022-11-21T14:41:59.107Z
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```
ra23mik
CC BY-SA 4.0
2022-11-21T15:56:42.043Z
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`?
terdon
CC BY-SA 4.0
2022-11-23T14:15:47.683Z
I solved it, I added my solution to the question.
ra23mik
CC BY-SA 4.0
2022-11-23T14:37:52.990Z
Great! But please post your solution as an answer instead so the question can be marked as slved.
terdon
CC BY-SA 4.0
2022-11-24T12:31:29.400Z
Thank you for doing it for me. Very new to stackoverflow as you might have guessed.
ra23mik
<bcftools>
Bcftools 1.16 able to add F_MISSING tag?
# 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.


---

