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3.4 years ago
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How do I get a vcf file containing germline information paired with tumor and normal
For CNVkit, In this part, vcf, I run mutect2 in the tumor match normal mode, and get a vcf file . Such as:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal tumor
chr1 1877032 . C T . PASS CONTQ=93;DP=26;ECNT=2;GERMQ=43;MBQ=27,20;MFRL=259,114;MMQ=60,60;MPOS=6;NALOD=1.04;NLOD=3.01;POPAF=6.00;SEQQ=12;STRANDQ=24;TLOD=6.96 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:11,0:0.083:11:8,0:3,0:0|1:1877032_
chr1 1877037 . C T . PASS CONTQ=93;DP=24;ECNT=2;GERMQ=40;MBQ=27,20;MFRL=262,114;MMQ=60,60;MPOS=1;NALOD=1.04;NLOD=3.01;POPAF=6.00;SEQQ=12;STRANDQ=25;TLOD=6.96 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:10,0:0.083:10:7,0:3,0:0|1:1877032_
chr1 6283447 . G A . PASS CONTQ=93;DP=66;ECNT=2;GERMQ=93;MBQ=26,20;MFRL=215,159;MMQ=60,60;MPOS=14;NALOD=1.15;NLOD=7.83;POPAF=6.00;SEQQ=12;STRANDQ=17;TLOD=6.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:29,0:0.036:29:14,0:15,0:20,9,0,0 0/1:35
But this vcf file has no germline information.
