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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!
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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
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Sheila Broad Institute admin
@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.
Answers
@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 Thanks so much for your help!!!