<p>I was expecting something like in this image:</p>

<p><a href="https://i.sstatic.net/fPBKD.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/fPBKD.png" alt="enter image description here"></a></p>

<p>But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters?</p>

<pre><code>chr1    19063526    0   T   TAGCTTAGAATGGGATGTC 0   0   DP=1;ECNT=1;MBQ=0,34;MFRL=0,193;MMQ=60,52;MPOS=1;POPAF=7.30;TLOD=4.20   GT:AD:AF:DP:F1R2:F2R1:SB    0/1:0,1:0.667:1:0,0:0,1:0,0,0,1
</code></pre>

<p>Command used: <code>gatk Mutect2 -R hg38.fa -I test.bam -O test.vcf.gz</code></p>

<pre><code>GATK -v4.1.2.0
Mutect2 version 2.2

Linux v4.15.0-1044
</code></pre>

CC BY-SA 4.0
2019-07-31T08:50:14.103Z
Please [edit] your question and add i) the exact command you ran on the file and iii) the version of the tool(s) you used and the operating system you ran them on and iii) a variant line from the output VCF file.
terdon
CC BY-SA 4.0
2019-07-31T09:58:24.387Z
@terdon It was edited, and now it includes what you asked for.
llrs
CC BY-SA 4.0
2019-07-31T10:03:26.193Z
What is the `**FILTER**`? Please show us an actual line from your file. If the FILTER field was emtpy, then leave it empty. We need to have a representative line from your file that shows the problem.
terdon
CC BY-SA 4.0
2019-07-31T10:06:42.600Z
chr1 19063526 0 T TAGCTTAGAATGGGATGTC 0 0 DP=1;ECNT=1;MBQ=0,34;MFRL=0,193;MMQ=60,52;MPOS=1;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,0,1
is the actual line
Vaishnavi Srinivasan
CC BY-SA 4.0
2019-07-31T10:12:28.603Z
Ah, OK thanks. So both FILTER and SCORE fields were `0`, then? Not empty?
terdon
CC BY-SA 4.0
2019-07-31T11:17:12.857Z
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php      This link has tumor-only mode option.
Vaishnavi Srinivasan
CC BY-SA 4.0
2019-07-31T12:30:20.433Z
Yes, sorry, my bad. I was looking at an older version. But please answer my previous question: were the FILTER fields empty or were they set to `0` as you show in your example?
terdon
CC BY-SA 4.0
2019-07-31T12:56:15.290Z
I didn't set to 0. The output itself is 0. I tried --RF [PASS] even then i get 0 as output for all variants.
Vaishnavi Srinivasan
<vcf><filtering>
Empty values in FILTER field after running Mutect2
# Empty values in FILTER field after running Mutect2

(Asked by: username_0 on 2019-07-31)

I was expecting something like in this image:

But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters?
chr1    19063526    0   T   TAGCTTAGAATGGGATGTC 0   0   DP=1;ECNT=1;MBQ=0,34;MFRL=0,193;MMQ=60,52;MPOS=1;POPAF=7.30;TLOD=4.20   GT:AD:AF:DP:F1R2:F2R1:SB    0/1:0,1:0.667:1:0,0:0,1:0,0,0,1

Command used: gatk Mutect2 -R hg38.fa -I test.bam -O test.vcf.gz
GATK -v4.1.2.0
Mutect2 version 2.2

Linux v4.15.0-1044

**Tags:** vcf, filtering
> **Comments:**
> **username_1**: Please [edit] your question and add i) the exact command you ran on the file and iii) the version of the tool(s) you used and the operating system you ran them on and iii) a variant line from the output VCF file.  
> **username_2**: @terdon It was edited, and now it includes what you asked for.  
> **username_1**: What is the `**FILTER**`? Please show us an actual line from your file. If the FILTER field was emtpy, then leave it empty. We need to have a representative line from your file that shows the problem.  
> **username_0**: chr1 19063526 0 T TAGCTTAGAATGGGATGTC 0 0 DP=1;ECNT=1;MBQ=0,34;MFRL=0,193;MMQ=60,52;MPOS=1;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,0,1 is the actual line  
> **username_1**: Ah, OK thanks. So both FILTER and SCORE fields were `0`, then? Not empty?  
> **username_0**: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php      This link has tumor-only mode option.  
> **username_1**: Yes, sorry, my bad. I was looking at an older version. But please answer my previous question: were the FILTER fields empty or were they set to `0` as you show in your example?  
> **username_0**: I didn't set to 0. The output itself is 0. I tried --RF [PASS] even then i get 0 as output for all variants.  

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## 0 answers

