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  • #31
    Originally posted by Ann Turner View Post
    Have you developed a systematic way to use the VCF files? The lack of data in the ID column(which should contain SNP names when known) and INFO column (which could contain tags for "novel", "on the tree", etc) makes it more difficult than necessary.
    Ann, yes I have.

    I've downloaded the ISOGG Ybrowse tool SNP database. Since I am only working on R1b today I filtered out everything that did not have the consecutive characters "R1b" or "M269" somewhere listed. If SNPs are properly entered that should get the R1b data set. I'm a little worried that some SNPs are not properly listed in Ybrowse. I thought Thomas Krahn said he entered all of the S series SNPs into Ybrowse but I have noticed one or two from the Chromo 2 anonymized 2000 file that I couldn't find. Maybe he didn't all of them and just the ones he felt were most relevant... or I'm just misreading the data. Here is this YBrowse "R1b" subset reformatted.
    https://dl.dropboxusercontent.com/u/...P_Cleanup.xlsm

    I took this R1b filtered SNP list and consolidated it so that one GRCh37 position/allele change variant will only appear once in a table with all of its labels beside it.
    Ex: 07340450C>T DF1/L513/S215

    For the Big Y .vcf files, I wrote two quick little macros for the .vcf files that automatically reformat the derived and passed variants into the same GRCh37 position/allele format and filter them to the top. I can then copy/paste those into another spreadsheet where I'm doing comparisons.

    I use the FTDNA kit number appended (actually prefixed) to each derived mutation in the above format to accumulate a large database (large # rows but only a couple of columns) of derived test results by individual. In that spreadsheet, on another tab, I have a summary/comparison table with the SNPs down one side of the table and the kit #s/surnames/Variety STR signatures on the 2nd dimension (across the top) of the table. Because I have the R1b Ybrowse SNP reference also in the same spreadsheet I add the labels (Ex: DF1/L513/S215) in the comparison table. Most of the new Big Y variants are unlabeled, which is good. We are discovering new stuff.

    I did have to compare two brother clades, L21 and U152, in my L21 comparative analysis to eliminate novel variants that must be upstream of either.

    I can now easily add .vcf to this comparative analysis and sort and filter them, etc. I've got 39 L21 .vcf files in the comparative analysis, but I had to have a system so the next 300 won't sink me.

    I imagine the U106 guys are doing something very similar. However, this only gets you a comparison of derived results. If you want to prove something is ancestral versus no call I think we'll have to use those .bam file. On the other hand, with a lot of individuals tested, you can overpower that need to some extent other than for final proofs.

    I'm trying to set this up so other project administrators can use it. I think it is inevitable this kind of stuff will be done at more youthful and more youthful subclade levels.
    Last edited by mwwalsh; 17 March 2014, 09:13 AM.

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    • #32
      Originally posted by mwwalsh View Post
      ...
      I've downloaded the ISOGG Ybrowse tool SNP database. Since I am only working on R1b today I filtered out everything that did not have the consecutive characters "R1b" or "M269" somewhere listed. If SNPs are properly entered that should get the R1b data set. I'm a little worried that some SNPs are not properly listed in Ybrowse. I thought Thomas Krahn said he entered all of the S series SNPs into Ybrowse but I have noticed one or two from the Chromo 2 anonymized 2000 file that I couldn't find. Maybe he didn't all of them and just the ones he felt were most relevant... or I'm just misreading the data. Here is this YBrowse "R1b" subset reformatted.
      ....
      Oh boy, I think this is the case. It appears that many of the S series SNPs added to Ybrowse don't have any haplogroups designated. Here are a couple of examples. Unfortunately I think there are a whole ton of S series SNPs entered without any haplogroup information. I don't have time to worry about the Ybrowse tool being correct.

      ID=Sequence:S10014;allele_anc=G;allele_der=A;prime r_f=TBD;primer_r=TBD;YCC_haplogroup=not+listed;
      ISOGG_haplogroup=not+listed;mutation=G+to+A;count_ tested=0;count_derived=0;ref=Jim+Wilson+(2014)

      ID=Sequence:S10015;allele_anc=C;allele_der=T;prime r_f=TBD;primer_r=TBD;YCC_haplogroup=not+listed;ISO GG_haplogroup=not+listed;mutation=C+to+T;count_tes ted=0;count_derived=0;ref=Jim+Wilson+(2014)

      Here is one I'm intimate with because its in me.
      ID=Sequence:S5196;allele_anc=T;allele_der=C;primer _f=TBD;primer_r=TBD;YCC_haplogroup=not+listed;ISOG G_haplogroup=not+listed;mutation=T+to+C;count_test ed=0;count_derived=0;ref=Jim+Wilson;comments=Aka.+ CTS5396

      Here is the synonym:
      ID=Sequence:CTS5396;allele_anc=T;allele_der=C;prim er_f=TBD;primer_r=TBD;YCC_haplogroup=not+listed;IS OGG_haplogroup=not+listed;mutation=T+to+C;count_te sted=0;count_derived=0;ref=Chris+Tyler-Smith+(2011);comments=Extracted+from+1000+genomes+ data.+Not+qualified.

      S5196/CTS5396 are clearly downstream of L21 and so far equivalent to R1b-L513. It looks like I'll have to weigh down the spreadsheet with all of these unknowns.

      Comment


      • #33
        Originally posted by MMaddi View Post
        The R1b-U106 Haplogroup Project has 12 Big Y results in so far, plus another 137 pending results.

        The Sicily Project has 7 pending Big Y results, 2 of which are also members of the R1b-U106 project.
        Good news for Big Y customers, at least in the R1b-U106 Haplogroup Project. Between today and yesterday, more than a dozen project members have received Big Y results. We now have 45 (29%) of the 153 Big Y results expected.

        Also, one of the Sicily Project members (also a R1b-U106 Project member) received his results.

        How did other projects fare since yesterday?

        Comment


        • #34
          Originally posted by MMaddi View Post
          How did other projects fare since yesterday?
          Before yesterday, the Polish Project had received only 12 BigY results.

          Yesterday and today, the project has received 14 BigY results.

          84 BigY orders remain outstanding, not counting full-price orders placed after the introductory period.

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          • #35
            The Milligan/Milliken project now has results for three members. That brings us to half completed. One had formerly been R-M222, one R-L48 and one R-Z159. We're waiting for three more R-M222s.

            Susan

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            • #36
              How has the Clan Donald project fared? badly:
              we have gotten back only 8 out of 57 BigY tests.

              And they are NOT coming back in order sent: they outright lied. We still have only ONE of the 8 ordered the first
              three days.

              The good news is that one is an R1a: one of 17 of those
              has now been delivered.

              I now can see why some people are not as upset about this
              as I am. One in 17 is not 29% delivered. Some projects
              are being favored, knowingly or not. I we had 29% delivered we would be feeling a lot better.

              Comment


              • #37
                Nine days left for about 75% or more of the total number of results?

                Doesn't seem very likely, does it?

                Comment


                • #38
                  Originally posted by DeeTyler View Post
                  Nine days left for about 75% or more of the total number of results?

                  Doesn't seem very likely, does it?
                  Could be one big release at the end of the month!

                  Comment


                  • #39
                    Big Y Progress

                    In my projects, we have 2 of 7 results received, so that's 28%.

                    Four of the five remaining orders were placed on 11/11 and 11/12, in Batch 542, the first batch. No Batch 542 results have been received yet.

                    Results have not been received in the order that orders were placed.

                    No new samples have been requested.

                    The last three scheduled completion dates for Big Y results have not been met. We have not been told why, so it is difficult to place any confidence in the currently scheduled 3/28 completion date.

                    Incidentally, pending test results still show Big Y gDNAQC for most of these orders scheduled to complete on 1/2/2014.

                    Comment


                    • #40
                      I ordered my Big Y on Nov 10 right after it was available in my FTDNA homepage thinking that I'll be among the first to get results. I was wrong

                      Comment


                      • #41
                        One of the things I noticed is that 2 of 3 kits in my project that aren't complete have very low kit numbers. I wonder if the age of the DNA sample can affect whether they pass quality control.

                        Susan

                        Comment


                        • #42
                          Originally posted by morrisondna View Post

                          The last three scheduled completion dates for Big Y results have not been met. We have not been told why, so it is difficult to place any confidence in the currently scheduled 3/28 completion date.
                          Did you pay attention to the statement FTDNA gave
                          We expect that all samples ordered during the initial sale (last November & December) will be delivered by March 28th. We are processing samples in first come first serve order. If a sample doesn't pass quality control, we will place it in the next set of results to be processed as long as we have enough DNA sample. If we require an additional sample, we will send a new test kit and place the new sample in the first set to be processed when it is returned.
                          This is not a promise, this not a commitment. And this is very clear - we were not given a promise as to the which is the delivery date.

                          If the expectations were wrong - then we will have a new date.

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                          • #43
                            Originally posted by similligan View Post
                            One of the things I noticed is that 2 of 3 kits in my project that aren't complete have very low kit numbers. I wonder if the age of the DNA sample can affect whether they pass quality control.
                            It is interesting that you noticed this. In my case, my sample was collected in Nov 2008. It was used for Y-37 and mtDNA Plus tests.

                            Over the next few years my sample was used for upgraded tests such as Y-67, Y-111, WTY, FGS, Y-HAP Backbone, 7 advanced DYS, 10 SNP tests, and Family Finder. None of these items ever appeared to have a problem with my stored sample(s).

                            In Nov 2014, I ordered the Big-Y test. It went into testing Batch 542. No problem notices were received (aside from revising test results due dates).

                            Then a package appeared in the mail with a letter (3/6/14) and a sample kit. Essentially the letter stated, "...we noticed during this process that you might have an older or scare sample. As a precautionary measure to avoid future delays we are sending you a new kit." The new sample was returned the next day.

                            Since then, nothing but silence. I know the new sample was delivered to FTDNA at Houston, TX and that's all. Queries to the FTDNA help desk have produced no additional information related to my Big-Y test results or the new sample.

                            Comment


                            • #44
                              Originally posted by Pillar_of_fire View Post
                              Did you pay attention to the statement FTDNA gave


                              This is not a promise, this not a commitment. And this is very clear - we were not given a promise as to the which is the delivery date.

                              If the expectations were wrong - then we will have a new date.
                              Yes. This note was in reply to a question as to whether it is likely the 3/28 date will be met. The scheduled dates that have been provided have changed four times so far and cannot be depended upon. I wish it was otherwise.

                              Comment


                              • #45
                                I signed up early for the Big Y test and I do not recall a contract that said "This will be done by ... ". It was clearly a volume Beta test, with a discount to encourage participation. The idea of a Beta is to get the bugs out of the system before a general release, and usually that is what happens, there are bugs and glitches. We who ordered the Big Y are all pioneers, early adopters, supposedly experienced users who understand the concept of Beta releases and willingly sign up to be on the almost bleeding edge of things. Pioneers like to get there and we will, but with a few interesting events along the way.

                                I think major projects often have both scope creep and expectation creep. And lots of learning experiences.

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