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I was expecting something like in this image:

enter image description here

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
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  • $\begingroup$ 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. $\endgroup$
    – terdon ♦
    Jul 31, 2019 at 8:50
  • $\begingroup$ @terdon It was edited, and now it includes what you asked for. $\endgroup$
    – llrs
    Jul 31, 2019 at 9:58
  • $\begingroup$ 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. $\endgroup$
    – terdon ♦
    Jul 31, 2019 at 10:03
  • $\begingroup$ 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 $\endgroup$
    – Vaishnavi Srinivasan
    Jul 31, 2019 at 10:06
  • $\begingroup$ Ah, OK thanks. So both FILTER and SCORE fields were 0, then? Not empty? $\endgroup$
    – terdon ♦
    Jul 31, 2019 at 10:12

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