New variants spreadsheet
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I have uploaded a new spreadsheet to
This likely has limited utility for anyone other than me, but I thought I'd share it. This file is used for analyzing Y-DNA mutation variants (SNPs, insertions/deletions, etc.) that us Z16357 people have. It's a very large spreadsheet with complex calculations - minor changes like sorting can take a long time to calculate. The Variants tab includes all 68,355 unique variants that we have. These were collected from Big-Y VCF files. You can use the Lookup tab to query specific DNA position numbers to see the values each of us have at that position. The Shared Variants tab shows all known variants ***AT OR BELOW Z16357*** that at least 2 of us have. This allows easy analysis of the consistency of SNPs and determination of their position on our branches. A "+" indicates a positive test for that variant. A "***" indicates the variant was identified, but the test quality is questionable. A blank box indicates EITHER a negative result OR no test coverage (be careful - you can't assume too much from a blank box without analyzing the BED file for read coverage). The Unique Variants tab lists most of the variants that are unique to only one of us. I'd be happy to add any new ones from YFull, if any of you who have tested there would like to e-mail them to me. Note that some Insertions/Deletions (these are kinda like hiccups in your DNA) show "Count" as 0 because Big Tree calculates the position info for INDELs a bit differently than the VCF file. These are retained for reference. The primary function of this spreadsheet is to easily add VCF data to Variants for new Big-Y testers, then immediately determine which existing SNPs from our branch they have, and which Unique Variants are then no longer unique and need to be moved to Shared Variants. Jared |
开云体育Addendum, there are actually more
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I assume that ambiguous is better than Low quality. Perhaps you do want the Ambiguous ones. Joel On 2/20/2017 6:44 PM, Jared Smith wrote: I have uploaded a new spreadsheet to This likely has limited utility for anyone other than me, but I thought I'd share it. This file is used for analyzing Y-DNA mutation variants (SNPs, insertions/deletions, etc.) that us Z16357 people have. It's a very large spreadsheet with complex calculations - minor changes like sorting can take a long time to calculate. The Variants tab includes all 68,355 unique variants that we have. These were collected from Big-Y VCF files. You can use the Lookup tab to query specific DNA position numbers to see the values each of us have at that position. The Shared Variants tab shows all known variants ***AT OR BELOW Z16357*** that at least 2 of us have. This allows easy analysis of the consistency of SNPs and determination of their position on our branches. A "+" indicates a positive test for that variant. A "***" indicates the variant was identified, but the test quality is questionable. A blank box indicates EITHER a negative result OR no test coverage (be careful - you can't assume too much from a blank box without analyzing the BED file for read coverage). The Unique Variants tab lists most of the variants that are unique to only one of us. I'd be happy to add any new ones from YFull, if any of you who have tested there would like to e-mail them to me. Note that some Insertions/Deletions (these are kinda like hiccups in your DNA) show "Count" as 0 because Big Tree calculates the position info for INDELs a bit differently than the VCF file. These are retained for reference. The primary function of this spreadsheet is to easily add VCF data to Variants for new Big-Y testers, then immediately determine which existing SNPs from our branch they have, and which Unique Variants are then no longer unique and need to be moved to Shared Variants. Jared
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Please send all of them (with an indication of or grouping by YFull's
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quality level). I'm curious how their quality levels align with those from the other sources I used - Mike W.'s analysis, Alex's Big-Y analysis, and my own. I don't really include much grading information in the spreadsheet, beyond FTDNA's read data (PASS or REJECTED, though they have an extremely high threshold for "PASS"), and the indication of the Region and STR data (anything in these columns will suggest lower quality). I didn't think it necessary to create a complex quality analysis metric in the spreadsheet seeing as this is what Mike, Alex, and YFull do best, and I can always reference their work in instances where things are questionable. Jared On Mon, Feb 20, 2017 at 4:56 PM, Joel Hartley <joel@...> wrote:
Thanks, Jared, |
Jared Smith