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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