U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Animal Genomics and Improvement Laboratory: Beltsville, MD
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                                    Software
                People

                    Staff Listing
                                    Careers


        


                    AIP
                        Home
                                    About
                                    Publications
                                    Software
                                    People
                                    Collaborations
                                    Careers
                                    Centennial
                                    Contact
                                    Dairy industry links
                    DirectionsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications
- IACUC
- Home
- About
- Publications
- Software
- People
- Collaborations
- Careers
- Centennial
- Contact
- Dairy industry links
- Home
- Queries login
- News
- Animal Evaluation lists
- Genotype counts

Title:   Author  item
                                            Bickhart, Derekitem
                                            HARRIS, LEWIN - University Of Californiaitem
                                            Liu, Ge

                                                         - *George*
  Submitted to: Journal of Dairy Science
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 2/23/2013
                                    Publication  Date: 7/8/2013
                                    Citation: Bickhart, D.M., Harris, L., Liu, G. 2013. Tools to exploit sequence data to find new markers and disease loci in dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):624 (abstr. 557).Interpretive Summary:
                                Technical Abstract: The decrease in cost of Next-Generation Sequencing has brought the technology into the realm of practical applications in livestock genomics. Recently, the 1000 Bulls Project has heralded the possibility of using full sequence data to improve imputation and detect disease loci within select founder bulls. Sadly, informatics tools designed to utilize such data have not yet reached maturity, as many currently available programs are hard-coded to call variants only in human subjects or take an inordinate amount of time for analysis. With these challenges and prospects in mind, we have developed a comprehensive variant detection pipeline that uses a variety of information derived from sequence data in order to call SNP, INDEL and structural variants within the genomes of individuals. The pipeline is designed to be fully automated, is capable of being restarted in the case of errors and can be run on different computing architectures. We have run our pipeline on sequence data derived from a famous Holstein bull. Despite having 87 gigabases (30X coverage of the genome) of sequence for this bull, our pipeline took only 48 hours to fully analyze the data using 20 processor cores and less than 32 gigabytes of ram. Initial filtering of this data has revealed one million candidate SNP and 759 copy number variants (CNV). An annotation program incorporated into the pipeline has also revealed putative functional impacts of these variants and has identified more than 17,000 non-synonymous SNP that could alter protein function in this individual. The pipeline provides an efficient and freely available tool for researchers to process cattle genomic sequence data to detect genetic variants for use in the dairy industry.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov