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gatk4: Mutect2 miss real variants
mauriziopolano
udineMember ✭
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!!!