Entering edit mode
8.1 years ago
umn_bist
▴
390
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...
- I do not see the same mutation (AA change).
- My variants are predominantly present in normal sample
- 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
It is an off question, but would you be so kind and unveil how did you get the bam files in first place?
Thanks