Three files used in this video: 1. The Excel file with the kits to Non-Matching Variants table: drive.google.com/open?id=1Eh-qL-OQvUmA0QlHUpPwIopXKJBGypER 2. The SAPP Input file template for mapping SNPs only: drive.google.com/open?id=1jM2hr5CW0t9HpqOI6md-tYHMUDA10Rfy 3. The Simple TMRCA calculator using weighted averages: drive.google.com/open?id=12r6ylOUe_2C8rEu7IZ500708eswx8gOB
One warning - for those of you comparing two or more Big Y700 tests (as opposed to Y500s), you can't use the 100 years per SNP that is used in the spreadsheet for TMRCA calculations at the end of the video. That number is smaller when comparing Y700 tests. There isn't a lot of data available yet about Y700 coverage, but for now use the number 82 in that year-per-SNP box. The spreadsheet makes it easy to change. Again that applies only if you are comparing two or more Y700 tests to each other. If you are comparing Y500s, or Y500s to Y700s, leave the number alone.
You will also notice that I changed the Non-Matching Variants Excel file linked in the pinned comment above to automatically show whether a particular variant is in any of 4 different definitions of "stable regions" of the Y chromosome. Those rows change depending on the position reference of the SNP in that column (not the name/label). That's for your use in deciding whether or not to use that variant in your branching decisions. In my view, any SNP which shows "N" for all four rows should probably not be used. A SNP that is "Y" in two or more definitions is probably ok. If it only shows "Y" in ONE row, it's PROBABLY ok but you have to decide. And some would argue that even the ones that show "N" in all four rows may be ok to use - I don't, but that's ok too. However, if you do see inconsistencies in the SNP results (either from SAPP or your own manual branching analysis), the SNPs that I would suspect first are the ones with fewer "Y" indicators.
David, can you recommend a read that goes into various steps of a DNA test? I am looking to understand how the DNA gets cut up into identifiable sections, how those sections are physically analyzed, etc. I am looking to understand the lab process.
My book has a chapter on the various testing options but it keeps the discussion relatively high-level and does not go into detail on the lab options. You might try this video link: ruclips.net/video/HBDms2vfP2Y/видео.html; it’s a presentation I gave earlier this year that can serve as an introduction to DNA testing and types of tests. It also pulls in a few vendor videos that give overviews of how various lab techniques work, both current and future. Otherwise there are lots of genetics videos available on how microarray tests, Sanger sequencing and Next Generation Sequencing (also called Massively Parallel Sequencing) work if you google those terms perhaps with “DNA test” after them. They’re not specific to genetic genealogy but they would serve as more detailed explanations of the lab processes. Microarray testing is how autosomal DNA works, the other two are different types of Y-DNA tests.
Peter if you look on my channel here I just put up a video describing at least at a high level the lab processes for various kinds of testing. That will probably not be enough but I did include links to further information. Hope that helps!
Any quick and dirty workarounds for the new CSVs downloadable from the BigY results page? Or will this still work with the Export Matches csv while on the Named or Private variants tabs? Thanks.
The CSVAnalysis tool should now work with the three new SNP CSV files that FTDNA provides for downloads. For the time being download all three and include them in the files for the CSVAnalysis tool run. You can also mix older files (the ones with all SNPs together) and the more recent Derived/Ancestral/NoCall files. For the time being all three files should be provided to CSVAnalysis at the same time. I doubt if the NoCall file is actually required but I'm still running tests to see what effect it has to not include it.
Question regarding downloading the CSV file: Has something changed since your video. You say go to the named variants tab and download the file. When I hit "download" it gives me 6 options (Export Matches, Export Derived SNPs, Export Ancestral SNPs, Export No Call SNPs, Download VCF, Buy Raw Data). Do I need to download multiple files (e.g. derived, ancestral, no call) to get the status of all SNPS? And hence do I need to ask testers for multiple CSV files to get what I need? Or is there somewhere to get all of what is needed with one CSV file. I may have missed something but have watched the video multiple times.
Sorry yes - FTDNA changed their downloads and split the SNP CSV into three parts. You now need to download three files from there - the Ancestral, Derived AND No-Call files and provide those to the CSVAnalysis tool (along with the STR one if you wanted to do that also). That’s new since the video and I do need to record a new video. Note that those CSV files are only useful if you were wanting to run the CSVAnalysis tool to either analyze the SNPs in your kits further or to format the STR and/or SNP sections to create a TXT file for input to SAPP. I’ve had people get confused and wanting to provide CSV files directly to SAPP so I always double-check that I haven’t also confused people on that too!
I'm at the step for identifying the SNP positions but am having problems. I have SNP FT28262 from a match but can't find the position. Your video says double click on the SNP to get the position from the browser. When I double click a SNP nothing happens. And when I go into the browser, it only shows my SNPs right? This SNP comes from a tester. Thanks in advance for your help.
You’re looking at YBrowse, right? Especially if you’re looking at it on an iPad or iPhone, that site has some problems with links, it’s better if you use a desktop. However you can also get to the detail page there with the direct link ybrowse.org/gb2/gbrowse_details/chrY/?name=FT28262 (or just copy that link and replace the ending SNP name with any other SNP to get to the detail page). That should show you that FT28262 is at position 5229822, which by the way is an X-transposed region that’s a little harder to read so make sure there are many (>10-15?) clear reads using the chromosome browser in FTDNA. I noticed also by the way that YBrowse seems to be running a little slow right now, there may be some server issues with it.
@@DaveVance01 Thank you Dave. Yes, I am using a desktop. I'll keep track (hopefully) of that link. My misunderstanding was just in reading YBrowse. I'd put in the SNP and it just seemed to keep coming back to the original screen but now I see that it does actually does show you the location. I assume there's a way to get to the detail display like the link you sent via that YBrowse screen. I've tried a lot of the options but haven't found the nice display like you sent yet. But as long as I keep your link, I'm good. And eventually I'll learn more about YBrowse. Thanks for your respone ... and thanks for your "... Y-DNA Testing for Genetic Genealogy" book. I've learned a lot. I'm sure I'll learn more on the second read ;-).
Three files used in this video:
1. The Excel file with the kits to Non-Matching Variants table: drive.google.com/open?id=1Eh-qL-OQvUmA0QlHUpPwIopXKJBGypER
2. The SAPP Input file template for mapping SNPs only: drive.google.com/open?id=1jM2hr5CW0t9HpqOI6md-tYHMUDA10Rfy
3. The Simple TMRCA calculator using weighted averages: drive.google.com/open?id=12r6ylOUe_2C8rEu7IZ500708eswx8gOB
One warning - for those of you comparing two or more Big Y700 tests (as opposed to Y500s), you can't use the 100 years per SNP that is used in the spreadsheet for TMRCA calculations at the end of the video. That number is smaller when comparing Y700 tests.
There isn't a lot of data available yet about Y700 coverage, but for now use the number 82 in that year-per-SNP box. The spreadsheet makes it easy to change.
Again that applies only if you are comparing two or more Y700 tests to each other. If you are comparing Y500s, or Y500s to Y700s, leave the number alone.
Thanks Dave. Interesting stuff. This may come in handy.
You will also notice that I changed the Non-Matching Variants Excel file linked in the pinned comment above to automatically show whether a particular variant is in any of 4 different definitions of "stable regions" of the Y chromosome. Those rows change depending on the position reference of the SNP in that column (not the name/label).
That's for your use in deciding whether or not to use that variant in your branching decisions. In my view, any SNP which shows "N" for all four rows should probably not be used. A SNP that is "Y" in two or more definitions is probably ok. If it only shows "Y" in ONE row, it's PROBABLY ok but you have to decide. And some would argue that even the ones that show "N" in all four rows may be ok to use - I don't, but that's ok too.
However, if you do see inconsistencies in the SNP results (either from SAPP or your own manual branching analysis), the SNPs that I would suspect first are the ones with fewer "Y" indicators.
David, can you recommend a read that goes into various steps of a DNA test? I am looking to understand how the DNA gets cut up into identifiable sections, how those sections are physically analyzed, etc. I am looking to understand the lab process.
David, does your book 'The Genealogist's Guide to yDNA testing' go into the lab process in detail?
My book has a chapter on the various testing options but it keeps the discussion relatively high-level and does not go into detail on the lab options. You might try this video link: ruclips.net/video/HBDms2vfP2Y/видео.html; it’s a presentation I gave earlier this year that can serve as an introduction to DNA testing and types of tests. It also pulls in a few vendor videos that give overviews of how various lab techniques work, both current and future.
Otherwise there are lots of genetics videos available on how microarray tests, Sanger sequencing and Next Generation Sequencing (also called Massively Parallel Sequencing) work if you google those terms perhaps with “DNA test” after them. They’re not specific to genetic genealogy but they would serve as more detailed explanations of the lab processes. Microarray testing is how autosomal DNA works, the other two are different types of Y-DNA tests.
Peter if you look on my channel here I just put up a video describing at least at a high level the lab processes for various kinds of testing. That will probably not be enough but I did include links to further information. Hope that helps!
Any quick and dirty workarounds for the new CSVs downloadable from the BigY results page? Or will this still work with the Export Matches csv while on the Named or Private variants tabs? Thanks.
The CSVAnalysis tool should now work with the three new SNP CSV files that FTDNA provides for downloads. For the time being download all three and include them in the files for the CSVAnalysis tool run. You can also mix older files (the ones with all SNPs together) and the more recent Derived/Ancestral/NoCall files.
For the time being all three files should be provided to CSVAnalysis at the same time. I doubt if the NoCall file is actually required but I'm still running tests to see what effect it has to not include it.
@@DaveVance01 Excellent, thank you very much!
Question regarding downloading the CSV file: Has something changed since your video. You say go to the named variants tab and download the file. When I hit "download" it gives me 6 options (Export Matches, Export Derived SNPs, Export Ancestral SNPs, Export No Call SNPs, Download VCF, Buy Raw Data). Do I need to download multiple files (e.g. derived, ancestral, no call) to get the status of all SNPS? And hence do I need to ask testers for multiple CSV files to get what I need? Or is there somewhere to get all of what is needed with one CSV file. I may have missed something but have watched the video multiple times.
Sorry yes - FTDNA changed their downloads and split the SNP CSV into three parts. You now need to download three files from there - the Ancestral, Derived AND No-Call files and provide those to the CSVAnalysis tool (along with the STR one if you wanted to do that also). That’s new since the video and I do need to record a new video.
Note that those CSV files are only useful if you were wanting to run the CSVAnalysis tool to either analyze the SNPs in your kits further or to format the STR and/or SNP sections to create a TXT file for input to SAPP. I’ve had people get confused and wanting to provide CSV files directly to SAPP so I always double-check that I haven’t also confused people on that too!
@@DaveVance01 Got it, thank you.
I'm at the step for identifying the SNP positions but am having problems. I have SNP FT28262 from a match but can't find the position. Your video says double click on the SNP to get the position from the browser. When I double click a SNP nothing happens. And when I go into the browser, it only shows my SNPs right? This SNP comes from a tester. Thanks in advance for your help.
You’re looking at YBrowse, right? Especially if you’re looking at it on an iPad or iPhone, that site has some problems with links, it’s better if you use a desktop. However you can also get to the detail page there with the direct link ybrowse.org/gb2/gbrowse_details/chrY/?name=FT28262 (or just copy that link and replace the ending SNP name with any other SNP to get to the detail page). That should show you that FT28262 is at position 5229822, which by the way is an X-transposed region that’s a little harder to read so make sure there are many (>10-15?) clear reads using the chromosome browser in FTDNA.
I noticed also by the way that YBrowse seems to be running a little slow right now, there may be some server issues with it.
@@DaveVance01 Thank you Dave. Yes, I am using a desktop. I'll keep track (hopefully) of that link. My misunderstanding was just in reading YBrowse. I'd put in the SNP and it just seemed to keep coming back to the original screen but now I see that it does actually does show you the location. I assume there's a way to get to the detail display like the link you sent via that YBrowse screen. I've tried a lot of the options but haven't found the nice display like you sent yet. But as long as I keep your link, I'm good. And eventually I'll learn more about YBrowse. Thanks for your respone ... and thanks for your "... Y-DNA Testing for Genetic Genealogy" book. I've learned a lot. I'm sure I'll learn more on the second read ;-).