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
                                            Liu, Ge

                                                         - *George*
  Submitted to: Meeting Abstract
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 1/11/2013
                                    Publication  Date: 1/11/2013
                                    Citation: Liu, G., Bickhart, D.M. 2013. Mapping cattle copy number variations in water buffalo. Meeting Abstract. W115.Interpretive Summary:
                                Technical Abstract: Copy number variation (CNV) is abundant in livestock, differing from SNPs in extent, origin and functional impact. Despite progress in CNV discovery, the nucleotide resolution architecture of most CNVs remains elusive. Using modified forms of open-source variant detection software packages, we have created a high throughput pipeline that detects SVs from paired-end NGS data in an efficient manner. Our pipeline uses previously reported SV detection strategies evaluated in the 1000 genomes pilot project such as read depth (RD), read pair (RP), split read (SR) and local assembly (AS). We also use an algorithm called "Precision Aware Merger" (PAM) to combine rare overlapping events and resolve conflicts in the output. As a demonstration of the power of this combined approach to variant discovery, we present preliminary data obtained from a survey of 14 water buffalo individuals. We show that our SV detection methods are complementary and do not share a significant overlap. We are doing extensive experimental validation using CGH arrays, qPCR experiments and SNP arrays. Our analytical framework and the results it produces will serve as resources for future genome resequencing and animal selection studies.


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