Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches

Table 3 Concordance between SNP chip and NGS data across all three duplicate removal methods are nearly identical

We compared the genotypes from NGS and matched SNP chip data to see if concordance varied by duplicate removal approaches. We performed this comparison for all variants and for ACMG variants only. Reported values are the percentage of total SNP chip genotypes called for a particular group (e.g., homozygous reference) that were correctly called by NGS for a given group. Exactly 99.97 % of genotypes called homozygous reference by SNP chip were also called homozygous reference by NGS across no dup, picard, and SAMTools. Similarly, 99.91 % of ACMG genotypes called homozygous reference by SNP chip were called identically by NGS. In the Table, homref: homozygous for the reference allele, het: heterozygous, and homalt: homozygous for an alternate allele

ISSN: 1471-2105