Whole Genome Sequencing of Affected German Shepherd Dogs

Three affected GSDs were selected for WGS: a black/tan female with German ancestry (SRR15446412), a white female from the Netherlands (SRR15446416), and a black/tan female from an American service dog breeding colony (SRR15446414). Resequencing of genomes from the latter two dogs was performed using an Illumina HiSeq X Ten, generating 2x150 bp paired-end reads. Total reads generated ranged from 861 to 869 million per sample. Paired-end reads were trimmed, aligned to the indexed reference (CanFam3.1), sorted, and indexed to be viewed in IGV [65 (link)] using the Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT platform [66 (link)]. WGS data for the third affected GSD were generated on an Illumina HiSeq 2000, with 2x125 bp paired-end reads. A total of 584 million reads were trimmed, aligned to CanFam3.1 with Bowtie2 [67 (link)], and sorted and indexed using SAMtools [68 (link)].