The question comes up all the time from people using DNA testing to find family, What about free software to compare DNA kits. GEDMatch.com is probably the most well known DNA comparison tool. You can upload your raw DNA from several DNA testing sources and run comparisons with millions of other DNA kits. GEDMatch is free unless you want to be a Tier 1 user which costs $10 per month. While not free, the cost is nominal. There are several free software to compare DNA kits. Has anyone done some good programming on comparing two DNA kits?, you bet. Free Software To Compare DNA Kits is available and in most cases easy to use.
At Genetic Genealogy Tools there is free software to compare DNA kits. Among the tools on this site are
Genetic Genealogy Kit
GGK CLI Import Tool
BAM Analysis Kit
BAM Analysis Kit is a bundle of genome tools that will analyse .BAM raw data file and outputs in file format similar to genetic genealogy companies. The goal of this kit to enable end users to analyse their own genome on their personal computer.
The tool provides the following output,
- genome_complete.txt.gz – Complete list from all confident sites
- genome_full_snps.txt.gz – Complete list of all known SNPs
- filtered-autosomal-o37-results.csv.gz – Filtered by Autosomal DNA SNPs tested by DNA companies
- filtered-x-chromosome-o37-results.csv.gz – Filtered by X DNA SNPs tested by DNA companies
- Admixture_Dodecad_Report.html – Dodecad dv3 Population Admixture Report
- Admixture_Eurogenes_Report.html – Eurogenes K=36 Population Admixture Report
- Admixture_Globe13_Report.html – Globe13 Population Admixture Report
- Complete_SNPs_y.csv – List of all identified Y-SNPs along with other columns
- ISOGG_Y_Haplogroup.txt – ISOGG Y-Haplogroup identification as on 1-Jul-2015
- MtDNA_Haplogroup.txt – Mt-DNA Haplogroup based on Build 15 (30 Sep 2012)
- MtDNA_Haplogroup_Report.html – Mt-DNA Haplogroup Report
- rCRS_mtDNA.txt – MtDNA mutations in rCRS format
- RSRS_mtDNA.txt – MtDNA mutations in RSRS format
- telomere.txt – Telomere length
- telseq.out – Telomere raw output file
- Variants_Y.txt – Y-DNA Novel Variants
- Y-STR_Markers.txt – Y-STR Markers
- Y_SNPs.txt – ISOGG Y-DNA SNPs
- bam_chr*.vcf.gz – VCF files if ‘Delete VCF after processing’ is unchecked.
Autosomal Pedigree Creator
If one has the CPU cycles to spare, I’m somewhat partial to Beagle. 23andMe based their phasing (for DNA-ancestry primarily) on modified version of it, and AncestryDNA likewise compares their implementation to it as baseline in their phased IBD code.
Other Free Software To Compare DNA Kits
https://faculty.washington.edu/browning/beagle/beagle.html (GPL license) It can do imputation, pseudo-phasing (the current version no longer models known parent-offspring relationships, if one wants to keep those consistent version 4 might be preferable. But yeah, that’s Java, really slow and heavy, so I think that’s actually different direction from where you’re going.
On the other end there’s PLINK2 https://www.cog-genomics.org/plink2/ibd (GPL as well) which is probably one of the fastest Identity By Descent calculators out there; actually I use PLKINK2 anyway for pre-detecting pedigree off unknown datasets before running Beagle (or did, with 4.0 where they were modeled) on them anyway. I’d call it “quick and dirty” but I don’t actually have any performance reference at hand right now smile emoticon
Note though that if indeed the task is to “compare TWO DNA-kits” only, then that one is quite straightforward and if done on-demand then performance isn’t even an issue. It will, however, be necessary to research and test for best thresholds on mis-matched SNP’s etc. In any case, next step is visualization, which – depending how nice visualization one is looking for – is actually the challenging part where I’m stuck myself currently just due to having no time besides my day-job smile emoticon.
These are a few of the best free software to compare DNA kits. Please contact us if you have other suggestions that would help others in this community.