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
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