Skip to main content

Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Table 2 Improving callability by reducing PCR cycles or using an improved variant calling pipeline

From: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

Analysis version Whole Genome Application 5.0.0 Whole Genome Application 6.0.0
PCR Cycles 2 3 4 5 2 3 4 5
Autosome mean coverage, X 30.4 30.5 30.1 30.1 30.0 30.3 31.2 31.5
Autosome callabilitya, % 95.5 95.6 95.5 95.4 96.8 96.8 96.8 96.8
Autosome coverage at 15X, % 97.6 97.7 97.6 97.6 97.8 97.9 98.0 98.0
Autosome exon coverage at 15X, % 99.4 99.4 99.3 99.3 99.4 99.4 99.4 99.4
SNV recall, % 97.0 97.0 97.0 96.9 98.8 98.8 98.8 98.8
SNV precision, % 99.9 99.9 99.8 99.8 99.8 99.8 99.8 99.8
Indel recall, % 93.2 92.5 91.4 90.2 95.0 94.9 94.7 94.4
Indel precision, % 96.6 95.9 94.5 92.9 98.0 97.9 97.6 97.2
  1. Libraries were prepared from 100 ng of NA12878. Data was generated on a HiSeq X (2 × 151 bp) and data analysis performed using the BaseSpace Sequence Whole Genome Sequencing Application. a Callability describes the percentage of base calls in the data set that pass the quality metrics required for making a genotype call; base quality, alignment quality, and minimum coverage levels are considered. SNV Single-nucleotide variant, Indel Insertion/deletion