1000 Bull Genomes 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.
Since its inception in 2012, the 1000 Bull Genomes Project has grown from 234 animals (3 breeds) and identifying 28.3 million genetic variants to more than 3,800 cattle (150+ breeds of Bos taurus and Bos indicus) and identifying >150 million filtered variants (Run 7).
Download a presentation describing the project [9.4MB .pptx] by Dr Amanda Chamberlain (2019).
Joining the project:
To join Run 8 of the 1000 Bull Genomes Project you are required to contribute BAM and GVCF (GATK genomic VCF) files for a minimum of 50 animals sequenced at 10x coverage after quality control (or 500x equivalent), and be approved by the project steering committee. Data submission deadline for Run 8 is 30-Nov-2019.
Project resources for Run 8:
- Reference genome: ARS-UCD1.2_Btau5.0.1Y
- File Submission Checklist [17KB .xlsx]
- Updated 1000 bulls GATK fastq to GVCF guidelines (GATKv3.8) [1.2MB .docx]
- Previous BQSR known variants file [495MB .vcf.gz], index [1.6MB .vcf.gz.tbi] and md5sums [1KB .txt]
- Updated BQSR known variants file (to be used for all new submissions including outspecies) [7.6GB .vcf.gz], index [2.3MB .vcf.gz.tbi] and md5sums [1KB .txt]
**NOTE** these resources can also be downloaded from AgVic's server (instructions can be found in the above guidelines)