RecView: An interactive R application for locating recombination positions using pedigree data

We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. We demonstrate applicability of RecView using the genotype data from two offspring, as well as their grandparents and parents, of the great reed warbler (Acrocephalus arundinaceus). Methods We randomly selected a three-generation pedigree, including 4 grandparents (Aarun_H7-38, Aarun_H0-81, Aarun_V9-73, Aarun_H7-41), 2 parents (Aarun_H3-00, Aarun_H5-17) and 2 offspring (ID-256 and ID-258), from our long-term study population of great reed warblers at Lake Kvismaren, southern Central Sweden (59°10ʹ N, 15°24ʹ E). The birds were whole-genome sequenced with Illumina. The sequence reads were trimmed, mapped to the great reed warbler genome assembly, and read duplicates were removed. Then, a VCF file of called variants were produced, and the genotypes at bi-allelic SNPs on chromosome 1 and 21 were extracted. In addition to the full dataset, we downsampled the number of SNPs to 10% and 1% of the original number (referred to as the “10% downsampled dataset” and “1% downsampled dataset”).