SNP FAQ Archive

This book contains actual questions asked by dbSNP and dbMHC users. We have tried to compile questions and answers that are representative of the entire spectrum of questions that our users ask, regardless of whether or not they are frequently asked. It is therefore likely that the question you have now, or a variant of it, may have been asked before, and may be in this book. The book will be updated with new questions regularly.

The questions and their answers have been edited for clarity and to protect the privacy of our users.

If you have a question about the SNP FAQ archive, or have a question you would like to see included in the archive, please contact vog.hin.mln.ibcn@nimda-pns

Contents

• dbSNP Submission Quick Start
  • Beginning the Submission Process
  • Choosing a Submission Format
  • VCF Submissions
  • Flat File Submissions
  • Submitting Data and Submission Processing
• Searching dbSNP for Variations and Variation Data
  • General dbSNP Search Options
  • Locating and Analyzing SNPs Associated with Disease Causing Mutations
  • Locating SNPs in a Gene or in Genes
  • Locating SNPs in (a) Chromosome(s)
  • Locating ENCODE (Encyclopedia Of DNA Elements) Project SNPs
  • Locating SNPs in a Protein Family
  • Searching for SNP Primer Sequences
  • Searching for SNPs in a NCBI Genome Build and in BAC Clones
  • Searching for a Class of Variations in dbSNP
  • Searching for SNPs or Specific SNP Data Using a Specific ID
  • Using SNP IDs to Find Genbank Accessions, and Vice Versa
  • Searching for SNPs Using Key Words, Names (Gene, Author, etc.), or Citations
  • Searching for SNPs Using Positional Data or EST Alignments
  • Retrieving Specific Data for a SNP
  • Searching for SNP Genotype, Allele and Frequency Data
  • Batch Query: Retrieving information for a large numbers of SNPs
  • Searching dbSNP using Sequence Data Homology (Search using BLAST)
  • Searching for SNPs in Raw Sequence Data
  • Searching for SNPs between Mouse Strains
  • Searching for Statistics, Data Histories and Historical Data in dbSNP
  • Searching for Structural (Copy Number) Variations
  • eSearch (Programmatic Searches)
  • Search Result Discrepancies
  • Errors that Occur While Searching
  • Unable to Find Published SNP in dbSNP
• Submitting Variations and Variation Data to dbSNP
  • Submission Handles
  • Requirements for dbSNP Submissions
  • Organism Data Accepted by dbSNP
  • Submitting Various Data Types to dbSNP
  • The dbSNP Excel Submission Template
  • Filling out the Submission Worksheets
  • Filling out Specific Sections/Fields within a Submission Worksheet
  • Submission Formatting
  • Automating the Submission Process
  • Submitting Information for Existing SNPs
  • Batch Submissions and Large Submissions to dbSNP
  • Submitting SNPs using a Reference Sequence Position
  • Submission and Assignment of Submitted SNP(ss)/RefSNP(rs) Numbers
  • dbSNP Submission Processing and the “Hold Until Published” (HUP) Policy
  • Submission Errors and Submission Withdrawal
  • Submission Using dbSNP’s online Clinical/LSDB Submission Resources
  • External Submission Tools
• Using dbSNP Data Reports
  • Entrez SNP and Entrez Gene Response Pages
  • Choosing the Data Report that Contains the Data You Need
  • Finding Information in a dbSNP Data Report
  • Compact SNP data: The Bitfield
  • Custom Report Formats
  • Interpreting Discrepancies in refSNP Reports
  • Interpreting Discrepancies in Submitted SNP (ss) Detail Reports
  • Discrepancies between Cluster Report Data and FTP Content
  • Discrepancies between Cluster Report data and Other Genome Resources
  • Field Definitions
  • SNP Class Definitions
  • Sequence Formatting in dbSNP Reports
  • Batch Reports
  • Displaying Reports
  • Links from dbSNP Reports to Other Online Data Resources
  • Links from Other Online Data Resources to dbSNP Reports
  • Creating Your Own Link to a dbSNP Record
  • Error Messages in refSNP Cluster Reports
• The dbSNP Build Process
  • What Triggers a New Build?
  • The SNP Build Schedule/Notification of Build Release
  • Data Changes that Occur Between Builds
  • Lag Time between dbSNP Website and FTP Site Following Build
  • The Difference Between the SNP Build and the Genome Build
  • Using Old vs. New Build Data
  • Finding Old Build Data
  • Finding a Build Number Based on a Date and Vice Versa
  • The dbSNP Mapping Process
  • Merging RefSNP Numbers and RefSNP Clusters
  • Ancestral Allele Data
  • Average Allele Frequency Calculation
  • Double Hit SNP Computation
  • Hardy Weinberg Equilibrium Data
  • Heterozygosity Data
  • Linkage Disequilibrium Data
  • dbSNP Haplotype Data
  • dbSNP and Haplogroup Data
  • dbSNP and Haplotype Tagged SNPs
  • dbSNP and HapMap Data
• Locating and Using Data from dbSNP’s FTP Site
  • Navigating in dbSNP’s FTP Site
  • Finding Specific Data in dbSNP’s FTP Files
  • SNP Report Files
  • dbSNP Data Dictionary
  • Missing FTP Files
  • Downloading From dbSNP’s FTP Site
  • Decompressing Data Obtained from dbSNP’s FTP Site
  • Parsing Data Obtained from dbSNP’s FTP Site
  • Discrepancies between dbSNP Summary Data and FTP Data
  • Discrepancies between Cluster Report Data and FTP Data Contents
  • Discrepancies between FTP Documentation and Data Dictionary
  • Direct Queries of dbSNP’s Database Server
  • Updating dbSNP’s FTP data
  • Eutils (E-utilities)
• dbSNP Organization and Structure (Schema)
  • Locating Schema Tables that Contain Specific SNP Data
  • SchemaTable Definitions/Locations
  • Field Definitions
  • Schema Changes and Updates
  • dbSNP Build Updates and Schema Changes
  • Downloading Specific Schema Tables
  • How does dbSNP draw the Schema Tables
  • Local Copies of dbSNP
• dbSNP Data Content Information
  • dbSNP Data Origins
  • dbSNP Data Quality Control
  • dbSNP Data Statistics
  • dbSNP Data Storage Information
  • Classes of Genetic Variation Included in dbSNP
  • Size of Genetic Variations Included in dbSNP
  • Sequence Notation for SNPs Housed in dbSNP
  • Submitted SNPs (ss) and Other Data Submitted to dbSNP
  • Clustered RefSNPs (rs) and Other Data Computed in House
  • Ancestral Allele Data
  • Association Studies
  • Ascertainment Bias
  • Automated SNP Collection (Data Mining)
  • Average Allele Frequency Calculation
  • Double Hit SNP Computation
  • Hardy Weinberg Equilibrium Data
  • Heterozygosity Data
  • Linkage Disequilibrium Data
  • References
• Citing dbSNP
  • Citing dbSNP in a Publication
  • dbSNP Creation Date Information
  • dbSNP Database Statistics
  • Using dbSNP data in a Locally Created Public Search Engine
  • Using Images from NCBI Sites
• General Information about dbSNP, Single Nucleotide Polymorphisims, and Genetics
  • General Information about dbSNP as a Database Resource
  • General information about Single Nucleotide Polymorphisms
  • Information about Haplotypes
  • dbSNP and Phenotype Records
  • STR Naming Convention
  • Evolution Questions
  • Pedigree Software
  • Personal Haplotype Questions
  • Personal SNP Screenings
  • Human Gene Nomenclature
• Human Variation Batch Submission Quick Start
  • Data Types Accepted in a Variation Batch Submission
  • Beginning the Submission Process
  • Using the Excel Submission Template to create your Batch Submission
  • Submitting Data
  • Submission Processing
  • Variation ID Assignment
  • Hold Until Published (HUP) Policy
  • How do I Update Data I’ve already Submitted?
  • How do I find my variations after submission, but before rs number assignment?
• Genome Workbench SNP Tools (GST) Quick Start
  • GST Defined
  • GST Features
  • Using GST for the First Time
  • Using Specific GST Features
  • Using GST to Study Genome Wide Association (GWAS) Data