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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 (not desktop tools)

website/page with no (desktop) 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

  • Borland Genetics Web Tools and Database Autosomal matching database with emphasis on reconstructing DNA of deceased individuals, linked to a set of DNA reconstruction tools for creating kits representing deceased ancestors
  • David Pike's Tools Utilities for analysing raw DNA data.
  • 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.
  • 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.).
  • YSEQ Phenotype Predictor A simple free tool to predict a number of physical features including eye colour, skin colour, hair colour, freckles, tanning and hair curliness.

Non-genealogical web tools

  • 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.
  • 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.

Desktop tools

  • Borland Genetics Desktop Toolkit Kevin Borland's free toolkit for reconstructing GedMatch-compatible synthetic DNA kits for deceased ancestors using raw DNA files of living relatives.
  • DNAGenics has numerous online and desktop tools for analyzing and manipulating Raw microarray data files. Originally known for their Windows desktop tool DNA Kit Studio but now also for admixture, haplogroup and other analysis services and tools.
  • dnamatch-tools. Python scripts "for working with various raw DNA files for genetic genealogy".
  • 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.
  • Golden Helix Genome Browser For details see Analyze your 23andMe genotype files with Golden Helix by Gabe Rudy, @gabeinformatics blog, 22 July 2015.
  • Reich Lab software A range of tools is available from the Reich Lab. These programmes are likely to be of interest to advanced users.
  • WGS Extract is a tool to extract Raw data (microarray test) and other files for phylogenetic tree analysis from whole genome sequencing BAM result files. (Windows, Linux and MacOS)

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 ToTheLetter DNA
Borland Genetics Yes Yes Yes No Yes No No Yes
Codegen 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 Yes
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

No longer available/supported/maintained

  • 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. (domain no longer exists)
  • GeneKnot A site which allows the user to upload genome data and compare DNA with other people with similar disease risks. (website not responding)
  • DNA.Land site no longer active
  • Gene Heritage no longer in business

See also