gatk4: Mutect2 miss real variants

mauriziopolano

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

Sheila

@mauriziopolano
Hi,

I think this was fixed in 4.0.4.0. The issue is that the PASS variants are not labeled with anything in the filter field in 4.0.3.0, but they are really PASS. In 4.0.4.0, you will see PASS in the filter field.

-Sheila

P.S. Have a look at this thread.

Sheila

@mauriziopolano
Hi,

I think this was fixed in 4.0.4.0. The issue is that the PASS variants are not labeled with anything in the filter field in 4.0.3.0, but they are really PASS. In 4.0.4.0, you will see PASS in the filter field.

-Sheila

P.S. Have a look at this thread.

mauriziopolano

@Sheila Thanks so much for your help!!!