What is your opinion on the differences between those two MuTect2 output ?

alaabadrealaabadre FranceMember
edited June 2017 in Ask the GATK team

Hello,

I am working on reproducing results from TCGA data on prostate cancer using MuTect2. I will state the main differences between their parameters and mine, and also some results:

  • They used GRCh38 (GRCh38.d1.vd1.fa) as a reference genome was modified by adding decoy and viruses sequences while I used hg19.
  • They decided to exclude the Chr7 intervals (intervals=[chr7:1-30000000]) whereas I excluded all intergenic and intragenic regions of the genome since we are working only on exome (by substracting the intervals of the library kit from the genome).
  • standard_min_confidence_threshold_for_calling = 30.0 (default in stable version is 10).

Other than that, I used the same dbsnp version, an newer cosmic version. As for the alignment files, I had to convert them back to FastQ and realign them again against hg19.

In one of the samples, they report a 31 that passed the filters only. As for mine, while the job is still running on the cluster and still on Chr7, the number of variants that passed the filters are 359 !

Any suggestion or opinion on why such difference would be appreciated, thanks in advance !

Alaa

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @alaabadre
    Hi Alaa,

    I suspect it is the difference in confidence threshold that is making the biggest impact. But, it is hard to tell without seeing some concrete examples. Can you post some example records that are called in your VCF but not in the other VCF?

    Thanks,
    Sheila

  • alaabadrealaabadre FranceMember

    Hello @Sheila,

    Sorry for the late reply. I've used a bedtools intersect (intersectBed -a TCGA.vcf -b mutect2.vcf) to show the common records by both output:

    chr9    14764   rs199668463 C   T   .   alt_allele_in_normal;panel_of_normals   DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=4.21;TLOD=8.03  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:30,2:0.083:1:1:0.500:901,62:18:12   0/1:9,7:0.400:4:3:0.429:277,164:3:6
    
    chr9    390636  rs10814649  A   G   .   germline_risk;panel_of_normals  DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=2.11;TLOD=6.92  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:7,0:0.00:0:0:.:212,0:1:6    0/1:1,2:0.667:1:1:0.500:32,68:0:1
    
    chr9    5762661 .   G   T   .   t_lod_fstar ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=7.52;TLOD=4.47 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:28,0:0.00:0:0:.:905,0:16:12 0/1:31,3:0.067:3:0:1.00:1013,101:12:19
    
    chr9    35906350    rs770170658 CCTGCTG C   .   alt_allele_in_normal;germline_risk;panel_of_normals DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=0.886;RPA=7,5;RU=CTG;STR;TLOD=21.48 GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:18,1:0.030:1:0:502,33:10:6  0/1:13,7:0.194:3:4:325,239:3:8
    
    chr11   281552  rs767854413 AGAG    A   .   alt_allele_in_normal;panel_of_normals;str_contraction;t_lod_fstar   DB;ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=26.43;RPA=5,4;RU=GAG;STR;TLOD=4.61  GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:123,3:9.709e-03:2:1:3881,92:64:59   0/1:152,5:0.017:5:0:4851,160:87:65
    
    chr11   1016789 .   T   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=144.75;TLOD=277.80  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2035,148:0.050:79:69:0.534:0|1:1016779_G_A:61311,4653:1004:1031 0/1:2343,166:0.047:81:85:0.488:0|1:1016779_G_A:72300,5343:1182:1161
    
    chr11   1016800 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=231.08;TLOD=288.08  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2424,155:0.043:83:72:0.535:0|1:1016779_G_A:77575,4859:1201:1223 0/1:2820,179:0.044:89:90:0.497:0|1:1016779_G_A:93561,5818:1415:1405
    
    chr11   1016802 .   T   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=262.02;TLOD=259.57  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2473,152:0.040:82:70:0.539:0|1:1016779_G_A:72128,4737:1223:1250 0/1:2886,178:0.040:88:90:0.494:0|1:1016779_G_A:85984,5739:1455:1431
    
    chr11   1016810 .   G   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=8;MAX_ED=90;MIN_ED=10;NLOD=297.33;TLOD=270.37  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:2672,151:0.039:83:68:0.550:85619,4502:1337:1335 0/1:3082,173:0.040:87:86:0.503:102266,5453:1553:1529
    
    chr11   1016835 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=13;MAX_ED=90;MIN_ED=10;NLOD=237.90;TLOD=337.05 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2794,180:0.046:86:94:0.522:0|1:1016818_A_G:87363,5853:1427:1367 0/1:3283,217:0.047:113:104:0.479:0|1:1016818_A_G:104632,7243:1644:1639
    
    chr11   1016836 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=14;HCNT=6;MAX_ED=90;MIN_ED=10;NLOD=679.92;TLOD=66.31   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:2773,27:0.00:11:16:0.593:88861,879:1395:1367    0/1:3318,33:6.149e-03:18:15:0.455:109162,1125:1659:1647
    
    chr11   1016845 .   C   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=2;MAX_ED=90;MIN_ED=10;NLOD=546.28;TLOD=27.27   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2802,101:0.015:45:56:0.554:0|1:1016845_C_G:92079,3283:1431:1371 0/1:3324,87:5.605e-03:35:52:0.598:0|1:1016845_C_G:113584,2966:1673:1651
    
    chr11   1016863 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=2;MAX_ED=90;MIN_ED=10;NLOD=456.26;TLOD=21.46   GT:AD:AF:ALT_F1R2:ALchr9    14764   rs199668463 C   T   .   alt_allele_in_normal;panel_of_normals   DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=4.21;TLOD=8.03  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:30,2:0.083:1:1:0.500:901,62:18:12   0/1:9,7:0.400:4:3:0.429:277,164:3:6
    
    chr9    390636  rs10814649  A   G   .   germline_risk;panel_of_normals  DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=2.11;TLOD=6.92  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:7,0:0.00:0:0:.:212,0:1:6    0/1:1,2:0.667:1:1:0.500:32,68:0:1
    
    chr9    5762661 .   G   T   .   t_lod_fstar ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=7.52;TLOD=4.47 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:28,0:0.00:0:0:.:905,0:16:12 0/1:31,3:0.067:3:0:1.00:1013,101:12:19
    
    chr9    35906350    rs770170658 CCTGCTG C   .   alt_allele_in_normal;germline_risk;panel_of_normals DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=0.886;RPA=7,5;RU=CTG;STR;TLOD=21.48 GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:18,1:0.030:1:0:502,33:10:6  0/1:13,7:0.194:3:4:325,239:3:8
    
    chr11   281552  rs767854413 AGAG    A   .   alt_allele_in_normal;panel_of_normals;str_contraction;t_lod_fstar   DB;ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=26.43;RPA=5,4;RU=GAG;STR;TLOD=4.61  GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:123,3:9.709e-03:2:1:3881,92:64:59   0/1:152,5:0.017:5:0:4851,160:87:65
    
    chr11   1016789 .   T   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=144.75;TLOD=277.80  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2035,148:0.050:79:69:0.534:0|1:1016779_G_A:61311,4653:1004:1031 0/1:2343,166:0.047:81:85:0.488:0|1:1016779_G_A:72300,5343:1182:1161
    
    chr11   1016800 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=231.08;TLOD=288.08  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2424,155:0.043:83:72:0.535:0|1:1016779_G_A:77575,4859:1201:1223 0/1:2820,179:0.044:89:90:0.497:0|1:1016779_G_A:93561,5818:1415:1405
    
    chr11   1016802 .   T   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=7;MAX_ED=90;MIN_ED=10;NLOD=262.02;TLOD=259.57  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2473,152:0.040:82:70:0.539:0|1:1016779_G_A:72128,4737:1223:1250 0/1:2886,178:0.040:88:90:0.494:0|1:1016779_G_A:85984,5739:1455:1431
    
    chr11   1016810 .   G   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=8;MAX_ED=90;MIN_ED=10;NLOD=297.33;TLOD=270.37  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:2672,151:0.039:83:68:0.550:85619,4502:1337:1335 0/1:3082,173:0.040:87:86:0.503:102266,5453:1553:1529
    
    chr11   1016835 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=13;MAX_ED=90;MIN_ED=10;NLOD=237.90;TLOD=337.05 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2794,180:0.046:86:94:0.522:0|1:1016818_A_G:87363,5853:1427:1367 0/1:3283,217:0.047:113:104:0.479:0|1:1016818_A_G:104632,7243:1644:1639
    
    chr11   1016836 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=14;HCNT=6;MAX_ED=90;MIN_ED=10;NLOD=679.92;TLOD=66.31   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:2773,27:0.00:11:16:0.593:88861,879:1395:1367    0/1:3318,33:6.149e-03:18:15:0.455:109162,1125:1659:1647
    
    chr11   1016845 .   C   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=2;MAX_ED=90;MIN_ED=10;NLOD=546.28;TLOD=27.27   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2802,101:0.015:45:56:0.554:0|1:1016845_C_G:92079,3283:1431:1371 0/1:3324,87:5.605e-03:35:52:0.598:0|1:1016845_C_G:113584,2966:1673:1651
    
    chr11   1016863 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=14;HCNT=2;MAX_ED=90;MIN_ED=10;NLOD=456.26;TLOD=21.46   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2325,83:0.017:37:46:0.554:0|1:1016845_C_G:72609,2692:1216:1109  0/1:2743,66:5.236e-03:28:38:0.576:0|1:1016845_C_G:87132,2255:1400:1343
    
    chr11   1016906 .   G   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=2;MAX_ED=57;MIN_ED=6;NLOD=94.21;TLOD=142.93 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:1204,89:0.049:50:39:0.562:0|1:1016906_G_T:38343,2834:614:590    0/1:1255,83:0.042:35:48:0.422:0|1:1016906_G_T:41207,2710:611:644
    
    chr11   1016912 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=2;MAX_ED=57;MIN_ED=6;NLOD=92.00;TLOD=132.30 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:1074,75:0.047:42:33:0.560:0|1:1016906_G_T:33910,2403:549:525    0/1:1064,75:0.044:28:47:0.373:0|1:1016906_G_T:34738,2428:529:535
    
    chr11   1016939 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=27.45;TLOD=61.94  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:639,58:0.066:32:26:0.552:0|1:1016939_G_A:19975,1881:310:329 0/1:555,38:0.045:14:24:0.368:0|1:1016939_G_A:17821,1281:269:286
    
    chr11   1016950 .   C   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=36.06;TLOD=46.87  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:595,33:0.057:19:14:0.424:0|1:1016939_G_A:18831,1069:301:294 0/1:522,24:0.034:8:16:0.667:0|1:1016939_G_A:17444,813:250:272
    
    chr11   1016951 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=58.60;TLOD=39.99  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:594,32:0.046:19:13:0.406:0|1:1016939_G_A:18940,1019:300:294 0/1:520,24:0.030:8:16:0.667:0|1:1016939_G_A:17030,801:245:275
    
    chr11   1016954 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=13.16;TLOD=89.83  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:541,50:0.033:30:20:0.600:17184,1313:277:264 0/1:480,44:0.033:13:31:0.295:15652,1220:235:245
    
    chr11   1016961 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=101.63;TLOD=20.67 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:551,21:0.012:11:9:0.550:0|1:1016939_G_A:17470,655:279:272   0/1:459,17:0.010:6:11:0.353:0|1:1016939_G_A:15179,592:225:234
    
    chr11   1016967 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals;t_lod_fstar  ECNT=3;HCNT=13;MAX_ED=9;MIN_ED=3;NLOD=141.49;TLOD=5.72  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:546,12:1.942e-03:5:7:0.417:17556,360:279:267    0/1:453,12:6.865e-03:4:8:0.333:15315,384:218:235
    
    chr11   1016970 .   C   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=3;HCNT=23;MAX_ED=9;MIN_ED=3;NLOD=78.96;TLOD=32.91  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:546,29:0.031:18:11:0.379:17471,913:275:271  0/1:460,23:0.029:8:15:0.652:15325,739:224:236
    
    chr11   1017974 .   C   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=7;HCNT=8;MAX_ED=50;MIN_ED=16;NLOD=126.65;TLOD=20.44    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:675,26:0.020:15:11:0.423:22095,836:360:315  0/1:649,22:0.016:11:11:0.500:22060,744:330:319
    
    chr11   1017979 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=7;HCNT=2;MAX_ED=50;MIN_ED=16;NLOD=155.64;TLOD=7.36 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:663,9:1.708e-03:5:4:0.556:21106,299:359:303 0/1:640,5:3.581e-03:4:1:0.800:21043,177:322:318
    
    chr18   677214  rs7229142   G   A   .   germline_risk;panel_of_normals  DB;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.902;TLOD=11.63    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:4,0:0.00:0:0:.:114,0:1:3    0/1:0,3:1.00:2:1:0.667:0,102:0:0
    
    chr18   3116517 rs370426885 TGA T   .   alt_allele_in_normal;panel_of_normals;str_contraction   DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=6.79;RPA=6,5;RU=GA;STR;TLOD=6.99    GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:47,3:0.030:1:2:1528,99:16:31    0/1:37,4:0.100:3:1:1230,133:16:21
    
    chr18   14779941    rs200991381 C   T   .   panel_of_normals    DB;ECNT=2;HCNT=4;MAX_ED=1;MIN_ED=1;NLOD=8.43;TLOD=16.55 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:27,0:0.00:0:0:.:0|1:14779941_C_T:888,0:16:11    0/1:28,5:0.161:4:1:0.200:0|1:14779941_C_T:949,159:11:17
    
    chr19   932466  rs745547598 TGAG    T   .   germline_risk;panel_of_normals;str_contraction  DB;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=2.07;RPA=6,5;RU=GAG;STR;TLOD=6.85   GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:8,0:0.00:0:0:251,0:2:6  0/1:9,2:0.200:2:0:254,69:5:4
    T_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:2325,83:0.017:37:46:0.554:0|1:1016845_C_G:72609,2692:1216:1109  0/1:2743,66:5.236e-03:28:38:0.576:0|1:1016845_C_G:87132,2255:1400:1343
    
    chr11   1016906 .   G   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=2;MAX_ED=57;MIN_ED=6;NLOD=94.21;TLOD=142.93 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:1204,89:0.049:50:39:0.562:0|1:1016906_G_T:38343,2834:614:590    0/1:1255,83:0.042:35:48:0.422:0|1:1016906_G_T:41207,2710:611:644
    
    chr11   1016912 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=2;MAX_ED=57;MIN_ED=6;NLOD=92.00;TLOD=132.30 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:1074,75:0.047:42:33:0.560:0|1:1016906_G_T:33910,2403:549:525    0/1:1064,75:0.044:28:47:0.373:0|1:1016906_G_T:34738,2428:529:535
    
    chr11   1016939 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=27.45;TLOD=61.94  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:639,58:0.066:32:26:0.552:0|1:1016939_G_A:19975,1881:310:329 0/1:555,38:0.045:14:24:0.368:0|1:1016939_G_A:17821,1281:269:286
    
    chr11   1016950 .   C   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=36.06;TLOD=46.87  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:595,33:0.057:19:14:0.424:0|1:1016939_G_A:18831,1069:301:294 0/1:522,24:0.034:8:16:0.667:0|1:1016939_G_A:17444,813:250:272
    
    chr11   1016951 .   A   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=58.60;TLOD=39.99  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:594,32:0.046:19:13:0.406:0|1:1016939_G_A:18940,1019:300:294 0/1:520,24:0.030:8:16:0.667:0|1:1016939_G_A:17030,801:245:275
    
    chr11   1016954 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=13.16;TLOD=89.83  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:541,50:0.033:30:20:0.600:17184,1313:277:264 0/1:480,44:0.033:13:31:0.295:15652,1220:235:245
    
    chr11   1016961 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=9;HCNT=3;MAX_ED=57;MIN_ED=6;NLOD=101.63;TLOD=20.67 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:551,21:0.012:11:9:0.550:0|1:1016939_G_A:17470,655:279:272   0/1:459,17:0.010:6:11:0.353:0|1:1016939_G_A:15179,592:225:234
    
    chr11   1016967 .   G   A   .   alt_allele_in_normal;clustered_events;panel_of_normals;t_lod_fstar  ECNT=3;HCNT=13;MAX_ED=9;MIN_ED=3;NLOD=141.49;TLOD=5.72  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:546,12:1.942e-03:5:7:0.417:17556,360:279:267    0/1:453,12:6.865e-03:4:8:0.333:15315,384:218:235
    
    chr11   1016970 .   C   T   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=3;HCNT=23;MAX_ED=9;MIN_ED=3;NLOD=78.96;TLOD=32.91  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:546,29:0.031:18:11:0.379:17471,913:275:271  0/1:460,23:0.029:8:15:0.652:15325,739:224:236
    
    chr11   1017974 .   C   G   .   alt_allele_in_normal;clustered_events;panel_of_normals  ECNT=7;HCNT=8;MAX_ED=50;MIN_ED=16;NLOD=126.65;TLOD=20.44    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:675,26:0.020:15:11:0.423:22095,836:360:315  0/1:649,22:0.016:11:11:0.500:22060,744:330:319
    
    chr11   1017979 .   G   C   .   alt_allele_in_normal;clustered_events;panel_of_normals;triallelic_site  ECNT=7;HCNT=2;MAX_ED=50;MIN_ED=16;NLOD=155.64;TLOD=7.36 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:663,9:1.708e-03:5:4:0.556:21106,299:359:303 0/1:640,5:3.581e-03:4:1:0.800:21043,177:322:318
    
    chr18   677214  rs7229142   G   A   .   germline_risk;panel_of_normals  DB;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.902;TLOD=11.63    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/0:4,0:0.00:0:0:.:114,0:1:3    0/1:0,3:1.00:2:1:0.667:0,102:0:0
    
    chr18   3116517 rs370426885 TGA T   .   alt_allele_in_normal;panel_of_normals;str_contraction   DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=6.79;RPA=6,5;RU=GA;STR;TLOD=6.99    GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:47,3:0.030:1:2:1528,99:16:31    0/1:37,4:0.100:3:1:1230,133:16:21
    
    chr18   14779941    rs200991381 C   T   .   panel_of_normals    DB;ECNT=2;HCNT=4;MAX_ED=1;MIN_ED=1;NLOD=8.43;TLOD=16.55 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1  0/0:27,0:0.00:0:0:.:0|1:14779941_C_T:888,0:16:11    0/1:28,5:0.161:4:1:0.200:0|1:14779941_C_T:949,159:11:17
    
    chr19   932466  rs745547598 TGAG    T   .   germline_risk;panel_of_normals;str_contraction  DB;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=2.07;RPA=6,5;RU=GAG;STR;TLOD=6.85   GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:8,0:0.00:0:0:251,0:2:6  0/1:9,2:0.200:2:0:254,69:5:4
    

    Now, if you look closely:

    in TCGA vcf:
    chr18 14779941 rs200991381 C T . panel_of_normals DB;ECNT=2;HCNT=4;MAX_ED=1;MIN_ED=1;NLOD=8.43;TLOD=16.55 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/0:27,0:0.00:0:0:.:0|1:14779941_C_T:888,0:16:11 0/1:28,5:0.161:4:1:0.200:0|1:14779941_C_T:949,159:11:17

    In my output:
    chr18 14779941 rs202240589 T G . PASS DB;ECNT=2;HCNT=4;MAX_ED=1;MIN_ED=1;NLOD=9.33;TLOD=16.55 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/1:28,5:0.161:4:1:0.800:0|1:14779940_C_T:919,172:12:16 0/0:31,0:0.00:0:0:.:0|1:14779940_C_T:1037,0:20:11

    So I suspect that the main reason here is probably the panel of normals that they have used to filter out most of the variants. I did not use any panel of normals in my pipeline since I was testing the reproducibility of 3 samples only (while they had more than 500).

    Am I correct ?

    Thank you, Sheila.

    Best regards,
    Alaa

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