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Raw DNA data tools

From ISOGG Wiki

Most of the major consumer genetic testing companies allow customers to download their raw data files. These files contain the “letters” (nucleotides A, C, G, T) that comprise DNA. The raw data can be uploaded to a variety of different services for free and/or paid analyses. The list below provides information on services which are of particular interest for genetic genealogy or which have been used by genetic genealogists. It is not intended to be a comprehensive list and is provided for information only. Inclusion on this list does not imply recommendation or endorsement by ISOGG.

Tool Category Meaning
web tools

website/page with no software installation needed

"genealogical"

can do analysis of a person's DNA against DNA from other relatives or ancestral populations
(e.g. ancestry/ethnicity/ancient DNA, compare/analyze relatives, find new relatives)

Genealogical web tools

  • David Pike's Tools Utilities for analysing raw DNA data.
  • DNAGedcom A website which provides a range of online and offline tools for analysing DNA data. The basic service is free. There is a monthly subscription fee for the premium service.
  • 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.
  • GEDmatch A free utility to compare autosomal DNA data files from all three testing companies and to compare Gedcom files. A number of other very useful tools are also provided, some for a fee.
  • Gene Heritage A service using raw DNA data to report on genes, traits, and ancient origins. Traits covered include eye color, lactose intolerance, alcohol flush reaction, and taste and smell sensitivity. Generates inheritance trees to show which genes were passed down from grandparents and parents to a child; identifies whether these genes originated in Europe, Asia, Eurasia, or Africa. Its Grandchild Report calculates what percentage of DNA a child inherited from each grandparent.
  • GENOtation 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.).
  • Wegene.com A Chinese company which provides an analysis of 23andMe results.

Non-genealogical web tools

Most of these tools are health related.

  • 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.
  • GeneKnot A site which allows the user to upload genome data and compare DNA with other people with similar disease risks.
  • Genetic Homeland Marker Index A free resource from Brad Larkin which provides an index of markers and their RSID positions on all 23 chromosomes.
  • HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool
  • 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. The site also provides an ethnicity calculator, height and hair colour predictors and a UK Biobank calculator.
  • Infinome A citizen science project that features a comprehensive interpretation engine for 23andMe data.
  • 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.
  • Xcode Life Xcode is a commercial company providing a range of health, trait, nutrition and fitness reports.

Non-web tools

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 Dante Labs
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

See also