Raw DNA data tools

GEDMATCH

Why is GEDMATCH missing from the DNA tools page?

If I understand correctly, it does take raw DNA data files so it should be on this page. I've gone ahead and added it to the list. --Castedo (talk) 13:14, 6 February 2019 (EST)

I know that GEDMATCH.com which labels itself as "Tools for DNA & Genealogy Research" is migrating to GENESIS. They report:

1/9/2019 Getting the message, "kit not found in the public DNA database"? Look in Genesis.

NOTICE: We are making progress on migration to the new Genesis site at genesis.gedmatch.com . Genesis will become the only GEDmatch.com at some point in the near future. This has become necessary because of the divergence of SNP sets used by various testing companies.

As of 12/18/2018 all new raw DNA kit uploads are only accepted by Genesis. The legacy GEDmatch site will continue to be available for some time, but results are "frozen" with all new kits being accepted, processed and results available only on Genesis.

The Genesis site can be accessed through a link at the bottom of the right column on this page, or directly by logging in at https://genesis.gedmatch.com

12/26/2018 We are pleased to say we have made contact with 23Mofang and GESEDNA (apparently two separate companies) and have begun to work with them to bring their results into compatibility with our algorithms.

April 28, 2018 While the database was created for genealogical research, it is important that GEDmatch participants understand the possible uses of their DNA, including identification of relatives that have committed crimes or were victims of crimes. If you are concerned about non-genealogical uses of your DNA, you should not upload your DNA to the database and/or you should remove DNA that has already been uploaded. Users may delete their registration/profile and associated DNA and GEDCOM resources. Instructions are available.

Call me curious. Jrcrin001 (talk) 13:12, 24 January 2019 (EST)

I think needs to be added to the GedMatch page.DebbieKennett (talk) 16:22, 24 January 2019 (EST)

Trisect Big Long List

The big long list is getting rather big and long. There is a desire to focus on genetic genealogy but it is hard to draw a precise line on what is or is not related to genetic genealogy.

I've visited all of the sites and can propose the following categorization which will trisect the list into sublists of no more than 10 entries.

This trisection uses just two criteria:

1) "web tool reading raw DNA files": A tool that can be used without having to install a computer program to read the common raw DNA data files, not requiring manual entry of contents of raw DNA data files.

2) "genetic genealogical": A tool that can a person's DNA to do analysis against DNA from other relatives or distant ancestral populations.

These two criteria can be used to roughly trisect the list into:

Category #1: genetic genealogy web tools reading raw DNA files

Category #2: non-genetic-genealogy web tools reading raw DNA files

Category #3: not web tools reading raw DNA files

Some of the REALLY advanced (and I think very hard to use tools) go into category #3 by this simple trisection, usefully I think.

What do people think?

I personally think it's confusing categorising the tools by the input method. I would suggest categorising tools by their output so that we have (1) tools providing genetic genealogy reports; (2) tools providing health and trait reports and (3) tools for analysing raw DNA data (eg phasing and conversion tools). Most of the really advanced tools would probably go in that latter category. In fact there is a new tool from Jef Treece that needs to be added: https://github.com/jeftreece/dnamatch-tools DebbieKennett (talk) 16:27, 9 February 2019 (EST)

Make sense to me that tool output usually gets closer to what readers care about more than tool input. For instance, distinguishing between manual input raw DNA data vs reading raw DNA files probably isn't worth the extra complexity. It only moves two links into the "other tools". I'll go ahead and move those tools and make the categorization simpler without the input distinction (and add Jef's tool) --Castedo (talk) 07:21, 10 February 2019 (EST)

Thinking about this again, there appears to be considerable overlap with the reports provided by the companies with some providing both health/trait and ancestry reports. I think the simplest solution might be to have two categories: (1) tools providing reports and (2) tools used for analysis. DebbieKennett (talk) 16:37, 9 February 2019 (EST)

The two challenges I had choosing categories for tools was (1) overalap and (2) subjective judgement.

So far, "web tool" is the only criterion I've been able to find that doesn't have an overlap issue and doesn't just create some small tiny list. Every other criteria I've come up with results in either a tiny list or overalap. Since ISOGG is all about genetic genealogy, my thought is that the overlap due to "genealogical" vs "health/trait" is worth it because we assume the #1 criterion most readers are interested in (or in a sense should be interested in) is whether the tool is "genealogical" or not. These criteria also has the benefit of spliting the big list into roughly similar sizes of sublists, no tiny lists.

"genealogical" has a subjective judgement challenge but I'm hoping this criterion is sufficiently objective:

 "can do analysis of a person's DNA against DNA from other relatives or ancestral populations"

Due to the other lap issue my thought is any other criteria other than "web tools" and "genealogical" should go into additional tables with green/red yes/no squares.

Do people want to explore adding another table with green/red yes/no squares to identify other criteria such as ancestry vs trait vs health vs free vs find-relatives, etc? It's more work so I'm kind of luke warm about it to be honest. --Castedo (talk) 08:17, 10 February 2019 (EST)

• • I think I might raise these issues in the ISOGG Facebook group to see if we can generate a wider discussion. I would define genealogical use as any tool that assists with the genealogical interpretation of DNA results. I would include in that phasing tools such as the Oxford phasing engine and also tools that provide trait reports. I suspect providing another table is going to be fraught with difficulties.DebbieKennett (talk) 08:43, 10 February 2019 (EST)

The Oxford phrasing engine is a great example of a tool that I'd consider right on the border of genealogical vs non-genealogical DNA analysis. By the criterion I proposed it falls outside the "genealogical" category, but I can see how this might be undesirable. I'll join Facebook so I can participate in the discussion. I suspect "traits" is going to be too subjective. --Castedo (talk) 10:17, 10 February 2019 (EST)

We do have some genetic genealogists at the forefront of citizen science who are experimenting with phasing. It is, after all, a way of getting better matches. I would suggest that traits should be focused on phenotype reports. After all AncestryDNA is rolling out trait reports so they are starting to become a part of the genealogy package. See what you think of the comments. It might be best to let the discussion run for a few days.DebbieKennett (talk) 15:59, 10 February 2019 (EST)

I apologize for changing the title of the section non-web to desktop before checking for a discussion on the issue. I didn't realize there was one. If you don't think that's an appropriate change, feel free to switch it back, but I thought the title was a bit negative and the purpose is to provide information as to what category the tools fall into, not to deter people from trying something because it might be advanced. Kborland (talk) 20:41, 8 April 2019 (EDT)

Seems to me more readers will understand "Desktop" than "Non-web". For that category of tools, "Desktop" seems a great pithy title. But it might not be clear that there is an objective bisection between "desktop" vs "web" tools. I'm thinking that at the very very top, when categories are introduced, some text of "(not desktop tools)" next to "web tools" will make this bisection more clear. I'll go ahead and add some text.

Technically, two of the non-web tools are scripts which can be run in a terminal session, server or desktop, and do not require a desktop. But I think this is a technically that is not worth worrying about. I bet people who run scripts on servers well still get it. --Castedo (talk) 07:02, 9 April 2019 (EDT)