1000 bull genomes project

The Project

The 1000 bull genomes project aims to provide, for the bovine research community, a large database for imputation of genetic variants for genomic prediction and genome wide association studies in all cattle breeds. The project aims to develop a resource to allow project partners to impute full genome sequence in bulls and cows that have been genotyped with SNP arrays. This could be used, for example, for improving the accuracy of genomic prediction, as well as in genome wide association studies interested in the identification of causal mutations.

Download a presentation describing the project [2MB .pdf] by Ben Hayes.

The Animals

Key ancestors of todays dairy industries have been selected for sequencing. The selected animals include a large number of Holstein bulls, but also includes Jerseys, Fleckvieh and Angus. Future runs will also include members of Brown Swiss, Ayrshire, and Simmental. The animals chosen for sequencing have contributed substantially to todays population. Having sequence data for these animals will allows the genomes of their descendants to be imputed up to full sequence level from SNP chip data. This means that the 100,000s of animals with SNP chip genotypes can now be imputed up to full sequence coverage, allowing more accurate GWAS and genomic predictions.

In January 2013 238 Bulls had been processed. Over 28 million SNP and Indels were identified in the dataset.

Hanoverhill Starbuck Valero

Download a database of bulls and cows that have been sequenced.

Project Resources

To join join the 1000 bull genomes project you are required to contribute a minimum of 25 animals sequenced at 10.5X coverage after quality control (or 250x equivalent), and be approved by the project steering committee.

Download the project's standard reference genome: umd_3_1_reference_1000_bull_genomes.fa.gz [768 MB]
or if you are in Europe: umd_3_1_reference_1000_bull_genomes.fa.gz     *Authentication Required

Download the Sequence Alignment Guidelines [24KB .docx] for producing BAM files for the 1000 bull genomes project
and the File Submission Checklist [16KB .xlsx].

Download variant annotations for SNPs [325MB .tab.gz] and INDELs [27MB .tab.gz] and a brief presentation [157KB .pdf] from 1000 Bull Genomes Run2 provided by Paul Stothard, University of Alberta

Example output files: