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Table 2 Comparison of calls made by the Genome Analysis Toolkit and QUAD GT on Quartet A.

From: Joint genotype inference with germline and somatic mutations

Normal genome  
Heterozygous SNPs (ref/alt) Homozygous SNPs (alt/alt)
called by both QUAD GT and GATK: 2100 called by both QUAD GT and GATK: 945
called by GATK only: 60 called by GATK only: 500
   QUAD GT calls ref/ref: 4    QUAD GT calls ref/ref: 0
   QUAD GT calls alt/alt: 9    QUAD GT calls ref/alt: 206
called by QUAD GT only: 839 called by QUAD GT only: 17
   GATK calls alt/alt: 206    GATK calls ref/alt: 9
De novo mutations  
called by both QUAD GT and GATK: 4  
called by GATK only: 327  
called by QUAD GT only: 0  
Tumor genome  
Heterozygous SNPs (ref/alt) Homozygous SNPs (alt/alt)
called by both QUAD GT and GATK: 2032 called by both QUAD GT and GATK: 938
called by GATK only: 41 called by GATK only: 504
   QUAD GT calls ref/ref: 3    QUAD GT calls ref/ref: 0
   QUAD GT calls alt/alt: 7    QUAD GT calls ref/alt: 224
called by QUAD GT only: 989 called by QUAD GT only: 17
   GATK calls alt/alt: 224    GATK calls ref/alt: 7
Somatic mutations  
called by both QUAD GT and GATK: 8  
called by GATK only: 512  
called by QUAD GT only: 6