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6.0 years ago
pinn
▴
210
Hi I called variants using mutect2 from normal and tumor samples. I'm surprised it showed all germ-line variants cant find single somatic variant . Whether I missed any parameters ? how to sort out this problem.
Thanks *Input *
Cancer type - breast
Normal bam size - 67 GB
Tumor bam size - 77 GB
Ref- hg38.fa
CMD-
java -Xmx32G -jar gatk-package-4.0.2.1-local.jar Mutect2 -I /data/cancer_samples/sample1/SAM/markduplicatesfixed_Realigned.normal.bam -normal NA12878 -O sample1_mutect2_normaltumor.vcf -R /data/Ref/hg38.fa -I /data/cancer_samples/sample1/SAM//markduplicatesfixed_Realigned.tumor.bam -tumor NA12878
Output-
sample1_mutect2_normaltumor.vcf - 25 mb
**VCF output **
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr1 16206 . T A . . DP=99;ECNT=2;NLOD=5.63;N_ART_LOD=10.07;POP_AF=1.000e-03;P_GERMLINE=-2.329e+00;TLOD=10.07 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:88,8:0.100:52,6:36,2:40:321,344:22:25
chr1 16263 . G C . . DP=102;ECNT=2;NLOD=15.02;N_ART_LOD=3.98;POP_AF=1.000e-03;P_GERMLINE=-1.374e+01;TLOD=3.98 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:94,6:0.071:49,3:45,3:39:318,317:20:44
chr1 55249 . C CTATGG . . DP=102;ECNT=1;NLOD=5.68;N_ART_LOD=12.14;POP_AF=1.000e-03;P_GERMLINE=-2.380e+00;TLOD=12.14 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:86,5:0.102:40,2:46,3:36:321,306:40:14
chr1 77568 . C A . . DP=48;ECNT=1;NLOD=4.58;N_ART_LOD=3.45;POP_AF=1.000e-03;P_GERMLINE=-3.830e+00;TLOD=3.45 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:40,2:0.105:22,1:18,1:36:325,332:43:3
chr1 84133 . A T . . DP=208;ECNT=1;NLOD=11.73;N_ART_LOD=25.43;POP_AF=1.000e-03;P_GERMLINE=-8.429e+00;TLOD=25.43 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:181,12:0.094:85,3:96,9:39:320,352:37:17
chr1 91486 . G C . . DP=48;ECNT=2;NLOD=5.44;N_ART_LOD=4.26;POP_AF=1.000e-03;P_GERMLINE=-3.892e+00;TLOD=4.26 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:46,2:0.042:17,0:29,2:39:320,321:27:15:0|1:91486_G_C
chr1 91490 . A G . . DP=51;ECNT=2;NLOD=6.05;N_ART_LOD=4.20;POP_AF=1.000e-03;P_GERMLINE=-4.550e+00;TLOD=4.20 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:48,2:0.049:19,0:29,2:39:319,321:27:11:0|1:91486_G_C
chr1 98753 . T C . . DP=173;ECNT=1;NLOD=37.48;N_ART_LOD=3.19;POP_AF=1.000e-03;P_GERMLINE=-3.699e+01;TLOD=3.19 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:159,3:0.050:78,0:81,3:39:326,327:38:11
chr1 98921 . AG A . . DP=117;ECNT=3;NLOD=22.24;N_ART_LOD=4.49;POP_AF=1.000e-03;P_GERMLINE=-2.046e+01;RPA=5,4;RU=G;STR;TLOD=4.49 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:112,4:0.037:53,2:59,2:34:320,326:34:24:0|1:98921_AG_A
chr1 98945 . C T . . DP=152;ECNT=3;NLOD=27.49;N_ART_LOD=5.85;POP_AF=1.000e-03;P_GERMLINE=-2.457e+01;TLOD=5.85 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:138,4:0.060:68,2:70,2:33:321,324:32:7:0|1:98921_AG_A
chr1 98999 . TTTTATTTA T . . DP=208;ECNT=3;NLOD=13.59;N_ART_LOD=3.50;POP_AF=1.000e-03;
