Atanas, The largest cost factor for Y chromosome tests is not the sequencing, but the enrichment procedure. With enrichment the price will never drop far below $400, so you might as well sequence with sufficient coverage. On the long run there is no future for BigY and FGCs Y tests since the WGS tests keep dropping in the price, but Y tests don't. Thomas On 01/06/2016 12:55 AM, Atanas Kumbarov via wrote: > I have exactly the same idea. If you have a tree to follow, you don't > need that many reads at a given position. But I think that it will be > better if FGC designs a Y-chromosome only test at 5x instead of WGS test > at 2x with the same price tag (around $250). The increase of depth of > coverage could be compensated by the decrease of sequenced locis (the > Y-chromosome only). > > 5x is sufficient - the 1000GP had 5x to 7x coverage and never the less > we see huge 1000GP dominated segments of the YFull tree like this one > http://yfull.com/tree/R-L657/ > > If such a test was offered, it could gain a lot of popularity. > > Best regards, > Atanas Kumbarov > > > > On 05/01/16 23:37, AJ Marsh via wrote: >> Tim, >> >> Many thanks for posting this. >> >> I have been waiting for some time to see what sort of results were coming from 2x coverage. I am a little bit encouraged by the figures from FGC. >> >> For the R-L617 project we have 20+ participants who have tested YElite or BigY. So we have a good tree starting to take shape of known SNPs below L617. >> >> If the 2x coverage test "covers" about 14,000,000 bases of Y, it might be too thinly covered to "confidently" call SNPs, as many of these bases will only be covered once. But in my case, I have a "work in progress" tree for mutations below L617, so reading the 2x coverage raw data might enable me to pick up mutations which are reported in raw data, but not reported more than once to enable FGC to call them confidently as a new SNP. >> >> My feeling is that in my case, where I have the advantage of a working SNP tree to compare to, it might be cost effective for me to extract benefit from the 2x coverage test. The area covered at least once by a 2x coverage test is more than half the area covered by YElite it seems. So if I can see matches to known L617 downstream and can call them, even at only 50% certainty, I should be able to tentatively place L617s into known branches. >> >> Several branches have 20+ known SNPS, so I only need one reliable call, or several less reliable calls of some of the 20+ branch SNPs to assign a tester to a branch, at least tentatively. Often there is already other forms of evidence pointing to a branch, so if it is corroborated to a degree by data from 2x coverage tests, it is a step forward. If in doubt, a SNP could be verified from single SNP testing. >> >> I think that I just need to have a few L617s tested on the 2x test to see how it works out in practice in my case. I feel optimistic. Although I am working on a SNP tree below L617, several haplogroup projects have similar type SNP trees building, so they might also get benefit. Cost of testing is always a challenge, so even if a 2x test is cutting corners a bit, it still might enable test to be done which otherwise might not be possible. >> >> John. >> >> Sent from my iPad >> >>> On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> wrote: >>> >>> Dear Atanas, >>> Justin Loe from FullGenomes just posted the information below on >>> another list: >>> >>> "As mentioned earlier, these are our beta results for 1x coverage: >>> >>> Mapped Y coverage >>> 30x 22,856,938 >>> 10x 22,025,697 >>> 4x 17,678,170 >>> 2x 13,755,442 >>> >>> Average Callable Loci >>> 30x 14,558,001 >>> 10x 8,046,540 >>> 4x 1,050,996 >>> 2x 349,397 >>> >>> Y Elite 2.0: >>> 14,000,000 Callable Loci approximately on average" >>> >>> This helps provide clearer data for your last question than I was able to do >>> in my earlier response. It thus appears that one needs to order at least >>> the 30x whole genome sequence from FullGenomes to get the same number of >>> callable Y chromosome loci as you can get from the Y Elite 2.0 test. >>> Sincerely, >>> Tim Janzen >>> >>> >>> -----Original Message----- >>> From: genealogy-dna-bounces@rootsweb.com >>> [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via >>> Sent: Tuesday, January 5, 2016 8:59 AM >>> To: genealogy-dna@rootsweb.com >>> Subject: [DNA] Full Genomes Corporation tests >>> >>> I have several questions about their tests: >>> >>> 1. I wonder how useful 2x results can be? >>> 2. What can be done with a FGS? >>> 3. Is it possible to extract usable data for GedMatch from FGS *in an easy >>> way*? >>> 4. How well is the Y-chromosome covered? >>> >>> Best regards, >>> Atanas Kumbarov >>> >>> >>> ------------------------------- >>> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message >> >> ------------------------------- >> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

All: I have the Big Y, a Full Genomes WGS at 3X, and the imputed VCF from my V3 23andMe results at DNA.Land. Who can compare the Y DNA results in all three files? I'd like to have it compared to another R1a with similar result files. After seeing the numbers in the post by Justin quoted by Tim, I will be increasing the coverage of the WGS file from Full Genomes. Steven On Tue, Jan 5, 2016 at 7:07 PM, Thomas Krahn via <genealogy-dna@rootsweb.com > wrote: > Atanas, > > The largest cost factor for Y chromosome tests is not the sequencing, > but the enrichment procedure. > With enrichment the price will never drop far below $400, so you might > as well sequence with sufficient coverage. > > On the long run there is no future for BigY and FGCs Y tests since the > WGS tests keep dropping in the price, but Y tests don't. > > Thomas > > > On 01/06/2016 12:55 AM, Atanas Kumbarov via wrote: > > I have exactly the same idea. If you have a tree to follow, you don't > > need that many reads at a given position. But I think that it will be > > better if FGC designs a Y-chromosome only test at 5x instead of WGS test > > at 2x with the same price tag (around $250). The increase of depth of > > coverage could be compensated by the decrease of sequenced locis (the > > Y-chromosome only). > > > > 5x is sufficient - the 1000GP had 5x to 7x coverage and never the less > > we see huge 1000GP dominated segments of the YFull tree like this one > > http://yfull.com/tree/R-L657/ > > > > If such a test was offered, it could gain a lot of popularity. > > > > Best regards, > > Atanas Kumbarov > > > > > > > > On 05/01/16 23:37, AJ Marsh via wrote: > >> Tim, > >> > >> Many thanks for posting this. > >> > >> I have been waiting for some time to see what sort of results were > coming from 2x coverage. I am a little bit encouraged by the figures from > FGC. > >> > >> For the R-L617 project we have 20+ participants who have tested YElite > or BigY. So we have a good tree starting to take shape of known SNPs below > L617. > >> > >> If the 2x coverage test "covers" about 14,000,000 bases of Y, it might > be too thinly covered to "confidently" call SNPs, as many of these bases > will only be covered once. But in my case, I have a "work in progress" > tree for mutations below L617, so reading the 2x coverage raw data might > enable me to pick up mutations which are reported in raw data, but not > reported more than once to enable FGC to call them confidently as a new SNP. > >> > >> My feeling is that in my case, where I have the advantage of a working > SNP tree to compare to, it might be cost effective for me to extract > benefit from the 2x coverage test. The area covered at least once by a 2x > coverage test is more than half the area covered by YElite it seems. So if > I can see matches to known L617 downstream and can call them, even at only > 50% certainty, I should be able to tentatively place L617s into known > branches. > >> > >> Several branches have 20+ known SNPS, so I only need one reliable call, > or several less reliable calls of some of the 20+ branch SNPs to assign a > tester to a branch, at least tentatively. Often there is already other > forms of evidence pointing to a branch, so if it is corroborated to a > degree by data from 2x coverage tests, it is a step forward. If in doubt, > a SNP could be verified from single SNP testing. > >> > >> I think that I just need to have a few L617s tested on the 2x test to > see how it works out in practice in my case. I feel optimistic. Although > I am working on a SNP tree below L617, several haplogroup projects have > similar type SNP trees building, so they might also get benefit. Cost of > testing is always a challenge, so even if a 2x test is cutting corners a > bit, it still might enable test to be done which otherwise might not be > possible. > >> > >> John. > >> > >> Sent from my iPad > >> > >>> On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> > wrote: > >>> > >>> Dear Atanas, > >>> Justin Loe from FullGenomes just posted the information below on > >>> another list: > >>> > >>> "As mentioned earlier, these are our beta results for 1x coverage: > >>> > >>> Mapped Y coverage > >>> 30x 22,856,938 > >>> 10x 22,025,697 > >>> 4x 17,678,170 > >>> 2x 13,755,442 > >>> > >>> Average Callable Loci > >>> 30x 14,558,001 > >>> 10x 8,046,540 > >>> 4x 1,050,996 > >>> 2x 349,397 > >>> > >>> Y Elite 2.0: > >>> 14,000,000 Callable Loci approximately on average" > >>> > >>> This helps provide clearer data for your last question than I was able > to do > >>> in my earlier response. It thus appears that one needs to order at > least > >>> the 30x whole genome sequence from FullGenomes to get the same number > of > >>> callable Y chromosome loci as you can get from the Y Elite 2.0 test. > >>> Sincerely, > >>> Tim Janzen > >>> > >>> > >>> -----Original Message----- > >>> From: genealogy-dna-bounces@rootsweb.com > >>> [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas > Kumbarov via > >>> Sent: Tuesday, January 5, 2016 8:59 AM > >>> To: genealogy-dna@rootsweb.com > >>> Subject: [DNA] Full Genomes Corporation tests > >>> > >>> I have several questions about their tests: > >>> > >>> 1. I wonder how useful 2x results can be? > >>> 2. What can be done with a FGS? > >>> 3. Is it possible to extract usable data for GedMatch from FGS *in an > easy > >>> way*? > >>> 4. How well is the Y-chromosome covered? > >>> > >>> Best regards, > >>> Atanas Kumbarov > >>> > >>> > >>> ------------------------------- > >>> To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > >> > >> ------------------------------- > >> To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > -- Steven C. 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