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.
Download a presentation describing the project [2MB .pdf] by Ben Hayes.
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 2,700 cattle (100+ breeds of Bos taurus and Bos indicus) and identifying >88 million filtered variants (Run 6).
Joining the project
To join Run 7 of the 1000 Bull Genomes Project you are required to contribute BAM and GVCF (GATK genomic VCF) files for a minimum of 25 animals sequenced at 10.5X coverage after quality control (or 250x equivalent), and be approved by the project steering committee. Data submission deadline for Run 7 is 30-Sep-2018.
Project resources for Run 7:
- Run 7 reference genome: ARS-UCD1.2_Btau5.0.1Y
- File Submission Checklist [17KB .xlsx]
- 1000 bulls GATK fastq to GVCF guidelines (GATKv3.8) [50KB .docx]
- 1000 Bulls BQSR Known Variants background information [394KB .docx]
- GATK BaseRecalibrator KnownVariants.vcf: ARS1.2PlusY_BQSR.vcf.gz and index ARS1.2PlusY_BQSR.vcf.gz.tbi
- Run 6 variant annotations for SNP [778MB .tab.gz] and INDEL [48MB .tab.gz] and a brief presentation [303KB .pptx] (provided by Paul Stothard, University of Alberta)