SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method.

ABSTRACT: We introduce a within-sample SNP calling method, called the "butterfly method", that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extremely important in forensic genetics and clinical diagnostics. This paper is accompanied by two open-source R packages, omni54manifest and snpbeadchip that make SNP calling easy by helping with bookkeeping and giving easy access to meta-information about the SNPs typed with the Illumina Infinium Omni5-4 Kit (including chromosome, probe type, and SNP bases). We compared the results from our method with those obtained with the Illumina GenomeStudio software (which does not provide sample and SNP spec

SUBMITTER: Andersen MM 

PROVIDER: S-EPMC9556601 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature