Table 4 Agreement between variant calling approaches on all called SNPs
From: Challenges in exome analysis by LifeScope and its alternative computational pipelines
Exome | Proband | Mother | Father |
|---|---|---|---|
Total number of SNP variants union of all approaches | 86,840 | 55,738 | 68,915 |
Number of SNP variants identified by all approaches common | 21,687 | 13,995 | 11,483 |
Fraction of common variants in total identified by LifeScope (%) | 56 | 40 | 32 |
LifeScope-GATK (%) | 32 | 44 | 25 |
MAQ-GATK (%) | 44 | 50 | 31 |
SHRiMP-GATK (%) | 32 | 36 | 27 |
BFAST-GATK (%) | 50 | 52 | 41 |
Number of SNP variants and fraction of total specific to LifeScope | 2936 (7.6 %) | 4543 (12.9 %) | 4246 (11.7 %) |
LifeScope-GATK | 5251 (8.7 %) | 4468 (10.2 %) | 4555 (9.7 %) |
MAQ-GATK | 1943 (3.9 %) | 1074 (3.8 %) | 1369 (3.7 %) |
SHRiMP-GATK | 14,276 (21.1 %) | 2210 (5.7 %) | 1644 (3.9 %) |
BFAST-GATK | 1097 (2.5 %) | 574 (2.1 %) | 9851 (35.2 %) |