Benchmark and Annotation New Canine Genome

SNIC 2022/6-199


SNIC Medium Storage

Principal Investigator:

Jennifer Meadows


Uppsala universitet

Start Date:


End Date:


Primary Classification:

30107: Medical Genetics



We aim to generate population level variation (single base and structural) data for >2,500 domestic and wild canids. This is a multi-centre collaboration across Europe and the US, using novel Illumina short read whole genome sequences (WGS), generated as part of the Dog 10K genomes project (, aligned to the Uppsala generated canine reference genome we generated (UU_Cfam_GSD_1.0). The Uppsala node expects to process 1/5 of the input data, and if resources allow, will process additional publically SRA WGS files. The bams and gvcfs generated in this effort will be shared within the consortia with GLOBUS or ftp, the vcf files will be available to the whole genomics community without embargo. Variation data will be hosted on UCSC and at additional sites (e.g. iDOG in China). The result will be a panel of normal variation, free available for the community to use. Our motivation for this project has its focus in health and medicine, both for the dog and as the dog for model of human health. It is expected that this data will rapidly aid the translation of variant association to causation through it use in variant elimination and the dissection of gene tolerance to variation.