Skip to main content

Table 1 Intersection of calls obtained using different alignment pipelines

From: Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

   TP - 100% NA12878a FP
BWA/GATK only (%) Intersection Novocraft only (%) BWA/GATK only (%) Intersection Novocraft only (%)
SNVs Mutect2 90 (1.1) 8435 91 (1.1) 23 (65.7) 12 15 (55.6)
Strelka 107 (1.3) 7928 37 (0.5) 12 (50.0) 12 5 (29.4)
Indels Mutect2 11 (6.4) 162 6 (3.6) 3 (60.0) 2 2 (50.0)
Strelka 7 (4.0) 169 3 (1.7) 0 (0.0) 2 8 (80.0)
  1. aOut of 9968 candidate SNVs and 420 true positive