Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

gatk4: Mutect2 miss real variants

Dear All,\
I use this version of GATK4 (4.0.3.0) and i follow the best practize and I filter as describe from the tutorial.

gatk-launch FilterMutectCalls -V {input.vcf} --contamination-table {input.cont} -O {output} -VS SILENT -LE;

No one variant are pass. The strange thing is I know there is a pathogenic deletion and vascan are able to see.
Mutect2 are able to see but not label pass. What is the problem here?

417 artifact_in_normal
      4 artifact_in_normal;base_quality
      1 artifact_in_normal;base_quality;clustered_events;mapping_quality;read_position
      1 artifact_in_normal;base_quality;clustered_events;mapping_quality;read_position;t_lod
     10 artifact_in_normal;base_quality;clustered_events;read_position
      1 artifact_in_normal;base_quality;clustered_events;t_lod
      1 artifact_in_normal;base_quality;mapping_quality;read_position;t_lod
      2 artifact_in_normal;base_quality;read_position
      5 artifact_in_normal;base_quality;read_position;t_lod
      2 artifact_in_normal;base_quality;strand_artifact
      1 artifact_in_normal;base_quality;strand_artifact;t_lod
      1 artifact_in_normal;base_quality;str_contraction
      9 artifact_in_normal;base_quality;t_lod
    534 artifact_in_normal;clustered_events
      1 artifact_in_normal;clustered_events;contamination;mapping_quality;read_position;t_lod
      1 artifact_in_normal;clustered_events;contamination;read_position;t_lod
     17 artifact_in_normal;clustered_events;fragment_length
      1 artifact_in_normal;clustered_events;fragment_length;t_lod
    194 artifact_in_normal;clustered_events;mapping_quality
      8 artifact_in_normal;clustered_events;mapping_quality;read_position
      1 artifact_in_normal;clustered_events;mapping_quality;read_position;t_lod
      6 artifact_in_normal;clustered_events;mapping_quality;strand_artifact
      2 artifact_in_normal;clustered_events;mapping_quality;str_contraction
      1 artifact_in_normal;clustered_events;mapping_quality;str_contraction;t_lod
     38 artifact_in_normal;clustered_events;mapping_quality;t_lod
      5 artifact_in_normal;clustered_events;multiallelic
     24 artifact_in_normal;clustered_events;read_position
      1 artifact_in_normal;clustered_events;read_position;strand_artifact
      4 artifact_in_normal;clustered_events;read_position;t_lod
      2 artifact_in_normal;clustered_events;strand_artifact
      3 artifact_in_normal;clustered_events;str_contraction
      1 artifact_in_normal;clustered_events;str_contraction;t_lod
    104 artifact_in_normal;clustered_events;t_lod
      1 artifact_in_normal;contamination;t_lod
      1 artifact_in_normal;fragment_length
      3 artifact_in_normal;fragment_length;mapping_quality
      1 artifact_in_normal;fragment_length;mapping_quality;read_position
      1 artifact_in_normal;fragment_length;mapping_quality;read_position;t_lod
      2 artifact_in_normal;fragment_length;t_lod
    188 artifact_in_normal;mapping_quality
      6 artifact_in_normal;mapping_quality;read_position
      4 artifact_in_normal;mapping_quality;read_position;t_lod
     10 artifact_in_normal;mapping_quality;strand_artifact
      1 artifact_in_normal;mapping_quality;str_contraction
      1 artifact_in_normal;mapping_quality;str_contraction;t_lod
     59 artifact_in_normal;mapping_quality;t_lod
     31 artifact_in_normal;multiallelic
      1 artifact_in_normal;multiallelic;read_position
      2 artifact_in_normal;multiallelic;str_contraction
     22 artifact_in_normal;read_position
      1 artifact_in_normal;read_position;strand_artifact
      1 artifact_in_normal;read_position;str_contraction
      4 artifact_in_normal;read_position;str_contraction;t_lod
     11 artifact_in_normal;read_position;t_lod
    216 artifact_in_normal;str_contraction
    101 artifact_in_normal;str_contraction;t_lod
    324 artifact_in_normal;t_lod
      1 base_quality
      2 base_quality;clustered_events
      1 base_quality;clustered_events;mapping_quality;read_position
      2 base_quality;clustered_events;read_position;t_lod
      1 base_quality;read_position
      4 base_quality;read_position;t_lod
      5 base_quality;t_lod
     90 clustered_events
      2 clustered_events;contamination;mapping_quality;t_lod
      1 clustered_events;fragment_length
      9 clustered_events;fragment_length;t_lod
     23 clustered_events;mapping_quality
      2 clustered_events;mapping_quality;read_position
     26 clustered_events;mapping_quality;t_lod
      9 clustered_events;read_position
      7 clustered_events;read_position;t_lod
      3 clustered_events;str_contraction
      1 clustered_events;str_contraction;t_lod
    120 clustered_events;t_lod
      4 fragment_length;t_lod
      9 mapping_quality
      2 mapping_quality;read_position
      7 mapping_quality;read_position;t_lod
      1 mapping_quality;str_contraction;t_lod
     23 mapping_quality;t_lod
      5 multiallelic
     14 read_position
     36 read_position;t_lod
     67 str_contraction
     89 str_contraction;t_lod
    629 t_lod

Mutecte2 report the fusion verify in this way:

        DP=370;ECNT=1;NLOD=51.25;N_ART_LOD=-2.248;POP_AF=5e-08;P_CONTAM=0.00;P_GERMLINE=-5.779e+01;TLOD=194.44  GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:120,54:0.324:60,30:60,24:34:177,180:60:23:0.263,0.303,0.31:0.086,0.005168,0.909 0/0:171,0:0.037:92,0:79,0:0:171,0:0:0
Tagged:

Best Answer

Answers

Sign In or Register to comment.