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

Dear John, If you get additional relatives on the paternal line of descent to test even at 2x the shared SNPs downstream from L617 become more valuable and more likely to be true SNPs than SNPs found only in one person's 2x results. A reasonable strategy might be to test two 1st, 2nd, or 3rd cousins who share the same surname at 2x and then test additional L617+ males who have different surnames as well. Sincerely, Tim -----Original Message----- From: AJ Marsh [mailto:ajmarshnz@gmail.com] Sent: Tuesday, January 5, 2016 2:38 PM To: Tim Janzen; genealogy-dna@rootsweb.com Subject: Re: [DNA] Full Genomes Corporation tests 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.

Good observations AJ. In the link I gave above to my Wiki NGS page the so far known stats seem to confirm your feeling also to me ;-) We have two 2x just ordered to see what they can provide. Wang, Wei et al 2011 <http://dx.doi.org/10.1038/srep00055> analysis suggests 3x is considerably better then 2x (the biggest coverage increase) when looking at low-coverage NGS. So I would like to see how much this could apply to the NGS lab used by FGC. Mind that you can upgrade later the FGC WGS tests to higher coverage. Justin is regularly posting in http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=130677&viewfull=1#post130677 Also I find the WGS very interesting for men who have not done mt or autosomal testing so far. On Tue, Jan 5, 2016 at 11:37 PM, AJ Marsh via <genealogy-dna@rootsweb.com> 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 >

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