I will be more than happy to examine your WGS 3x data together with your Big Y data. Best regards, Atanas Kumbarov On 06/01/16 01:28, steven perkins via wrote: > 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 >> > >

I taught DNA.Land's imputation VCF of 23andMe data covers only recombing genome parts (autosomal/X)? Please let us know about stats and comparison of WGS 3X with BigY. Good research. On Wed, Jan 6, 2016 at 8:41 AM, Atanas Kumbarov via < genealogy-dna@rootsweb.com> wrote: > I will be more than happy to examine your WGS 3x data together with your > Big Y data. > > Best regards, > Atanas Kumbarov > > On 06/01/16 01:28, steven perkins via wrote: > > 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 > >> > > > > > > > ------------------------------- > 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 >