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[cBioPortal] [GATK] [TCGA] Somatic variant calling error

So I have a tumor:match normal sample from TCGA for somatic variant calling using MuTect2.

According to cBioportal, I should see a K319Rfs*26 with an allele frequency for this patient at 0.37. Mind you, variants on cBioportal are not called against its respective matched normal.

When I call variants against its matched normal, however, and using dbSNP, COSMIC...

  1. I do not see the same mutation (AA change).
  2. My variants are predominantly present in normal sample
  3. My variants have embarassingly low AF (< 0.05) whereas ones for TCGA (at cbioportal) are all relatively high >0.3

I suspect that it's not cBioportal that's incorrect and it's me that's making a huge mistake in my pipeline.

My results:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  PRAD

    1   150900333   .   T   C   .   alt_allele_in_normal;clustered_events;t_lod_fstar   ECNT=2;HCNT=4;MAX_ED=56;MIN_ED=56;NLOD=23.85;TLOD=4.04  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:105,2:0.019:0:2:0.00:4057,74:51:54
    1   150900389   .   T   C   .   alt_allele_in_normal;clustered_events   ECNT=2;HCNT=4;MAX_ED=56;MIN_ED=56;NLOD=17.57;TLOD=6.39  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:96,3:0.030:3:0:1.00:3710,108:51:45
    1   150902490   .   T   C   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=24.15;TLOD=5.83    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:117,3:0.025:2:1:0.667:4497,105:57:60
    1   150913836   .   C   T   .   alt_allele_in_normal;clustered_events;t_lod_fstar   ECNT=2;HCNT=2;MAX_ED=47;MIN_ED=47;NLOD=25.51;TLOD=4.09  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:111,2:0.018:1:1:0.500:4189,75:52:59
    1   150913883   .   A   G   .   alt_allele_in_normal;clustered_events;t_lod_fstar   ECNT=2;HCNT=2;MAX_ED=47;MIN_ED=47;NLOD=10.37;TLOD=6.17  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:70,3:0.041:0:3:1.00:2702,108:36:34
    1   150917537   .   T   C   .   alt_allele_in_normal    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=21.09;TLOD=6.53    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:109,3:0.027:2:1:0.667:3975,111:45:64
    17  7571856 .   T   C   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=15.27;TLOD=5.83    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:86,3:0.034:2:1:0.667:3348,101:37:49
    17  7571931 .   T   C   .   alt_allele_in_normal;clustered_events   ECNT=3;HCNT=12;MAX_ED=95;MIN_ED=73;NLOD=30.37;TLOD=6.94 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:142,3:0.021:0:3:0.00:5413,120:69:73
    17  7572004 .   T   C   .   alt_allele_in_normal;clustered_events   ECNT=3;HCNT=12;MAX_ED=95;MIN_ED=73;NLOD=10.41;TLOD=22.71    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:151,9:0.056:6:3:0.667:5914,343:75:76
    17  7572026 .   T   C   .   alt_allele_in_normal;clustered_events   ECNT=3;HCNT=12;MAX_ED=95;MIN_ED=73;NLOD=37.77;TLOD=9.07 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:181,4:0.022:0:4:0.00:6714,156:94:87
    17  7572250 .   A   G   .   alt_allele_in_normal    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=34.46;TLOD=7.62    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:164,4:0.024:2:2:0.500:6305,139:85:79
    17  7572544 .   T   C   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=32.92;TLOD=5.27    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:146,3:0.020:3:0:1.00:5742,102:71:75
    17  7572677 .   A   G   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=37.33;TLOD=5.49    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:161,3:0.018:0:3:1.00:6135,108:75:86
    17  7573975 .   T   C   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=37.68;TLOD=4.04    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:152,2:0.013:1:1:0.500:5851,78:70:82
rna-seq gatk cbioportal tcga
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written by umn_bist • umn_bist

It is an off question, but would you be so kind and unveil how did you get the bam files in first place?

Thanks

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written by H.Hasani H.Hasani

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