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 |