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Raw DNA data tools

From ISOGG Wiki

These tools use raw DNA data files. Major DNA testing services like AncestryDNA, 23andMe, and FamilyTreeDNA allow customers to download raw DNA data files. These files contain the “letters” (nucleotides A, C, G, T) that comprise DNA.

Comparison by Raw DNA Data Sources

DNA testing services provide raw DNA data in different file formats.

DNA Testing Service
Raw DNA data tool (compatible with...) 23andMe Family Tree DNA Family Finder AncestryDNA National Geographic Geno 2.0 MyHeritage Living DNA Genes for Good Vitagene
Codegen Yes No No No No No No No
DNA Fit Yes No No No No No No No
DNA.Land Yes Yes Yes No No No No No
Infinome Yes No No No No No No No
Impute.me Yes Yes Yes Yes Yes Yes Yes No
Gene Heritage Yes Yes Yes Yes Yes Yes Yes No
openSNP Yes Yes No No No No No No
Promethease Yes Yes Yes Yes Yes Yes Yes No
WeGene Yes No Yes No No No No No
Xcode Yes Yes Yes Yes Yes Yes Yes Yes

List of Raw DNA Data Tools

  • David Pike's Tools Utilities for analysing raw DNA data.
  • DNA Fit A commercial company which accepts uploads of 23andMe data and will provide a report for a fee on diet, fitness, sports and wellbeing.
  • Codegen A free comprehensive health report using 23andMe raw data.
  • DNA.Land A not-for-profit community website run by academics affiliated with Columbia University and the New York Genome Center. The site offers a biogeographical analysis, imputation and a relative-matching feature.
  • Extracting a 23andMe V3 file from a whole genome BAM file Thomas Krahn has developed a script to generate a 23andMe file from a whole genome sequence to allow the user to upload the file to GEDMatch and other third-party tools.
  • Gene Heritage A service using raw DNA data to compile reports about how genes influence traits. Traits covered include eye color, earwax type, armpit odor, lactose intolerance, Asian Flush, and taste and smell sensitivity. Identifies the ancient origins of genes; reports on whether certain alleles originate in Europe, Asia, Eurasia, or Africa. Users can see how genes have been passed down from parents to a child.
  • GeneKnot A site which allows the user to upload genome data and compare DNA with other people with similar disease risks.
  • Golden Helix Genome Browser For details see Analyze your 23andMe genotype files with Golden Helix by Gabe Rudy, @gabeinformatics blog, 22 July 2015.
  • Impute.me A not-for-profit service run by Danish geneticists. Provides imputation combined with extensive trait analysis based on polygenic risk scores for all common diseases.
  • Infinome A citizen science project that features a comprehensive interpretation engine for 23andMe data.
  • Interpretome A set of online tools from Stanford University for analysing your personal genomic data. For further explanation see this blog post by Daniel MacArthur.
  • lineage A tool provided by Andrew Riha for analysing raw data files. There are options to merge raw data files from different DNA testing companies, compute centiMorgans of shared DNA between individuals using HapMap tables, plot shared DNA between individuals, determine genes shared between individuals, find discordant SNPs between child and parent(s), and remap SNPs between assemblies / builds (e.g., convert SNPs from build 36 to build 37, etc.).
  • Livewello Provides health and trait reports using raw data from 23andMe, AncestryDNA and FTDNA for physicians and advanced users. Twenty reports are provided free of charge with the Livewello Gene App. A subscription is required to access the manually curated health reports. The website also offers free health record managers and data charting applications.
  • NCBI Genome remapping service
  • OpenSNP OpenSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.
  • Oxford Statistics Phasing Server A free utility to phase whole genomes based on VCF files.
  • Promethease Accepts data from any genetic genealogy company and will generate health and trait reports based on current literature.
  • Reich Lab software A range of tools is available from the Reich Lab. These programmes are likely to be of interest to advanced users.
  • Wegene.com A Chinese company which provides an analysis of 23andMe results.
  • Xcode Life Xcode produces thoroughly curated, easy to understand genetic reports that can be used by professional practitioners as well as individuals. They can re-analyze data from 23andme, AncestryDNA, FTDNA, MyHeritage, Vitagene, Dante Labs among several other companies.

See also