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
                                            Vanraden, Paulitem
                                            Bickhart, Derek
  Submitted to: Plant and Animal Genome Conference Proceedings
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 1/8/2016
                                    Publication  Date: 1/8/2016
                                    Citation: Van Raden, P.M., Bickhart, D.M. 2016. Fast single-pass alignment and variant calling using sequencing data. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W161.Interpretive Summary:
                                Technical Abstract: Sequencing research requires efficient computation. Few programs use already known information about DNA variants when aligning sequence data to the reference map. New program findmap.f90 reads the previous variant list before aligning sequence, calling variant alleles, and summing the allele counts for each DNA source in a single pass. Advantages are faster processing, more precise alignment, more useful data summaries, more compact output, and fewer steps. Programs findmap and BWA were compared using simulated paired end reads of length 150 from fragments of length 1,000 at random locations within the UMD3.1 bovine reference assembly. Each base had 1% probability of error and 1% probability of missing. The 39 million variants from run 5 of the 1,000 bull genomes project were included, with every other variant set to reference or alternate. With 1 processor, BWA required 629 minutes per 1X for alignment, whereas findmap required 2 minutes per 1X for alignment and variant calling. Percentage of correctly mapped reads was 90.5% from BWA and 92.9% from findmap. Variant calls were output by findmap only for the 88.2% of pairs where both ends were located within the fragment length and of opposite orientation. Percentages of variants called correctly were 99.8% for SNPs and 99.9% for deletions, while insertions had 99.9% of alternate calls correct but only 98.6% of reference calls. Memory required by BWA was 4.6 Gbytes / processor, whereas findmap required 46 Gbytes that could be shared by multiple processors. Simultaneous alignment and variant calling is an efficient and accurate strategy.


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