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View Full Version : BigY move to hg38



simdadams
10-21-2017, 04:14 PM
Is this likely to affect us greatly ? Will we move haplogroups?

leonardo
10-21-2017, 04:24 PM
I don't believe so, for me. Most of those close to my on my BigY list (not yet updated, for me) have tested with YFull. My closest match there is 700 years in TMRCA. I suspect my revised BigY classification will align with the Yull, which is currently at least 2 branches down from what FTDNA says.

rms2
10-22-2017, 12:09 AM
I'm not sure what we'll get out of this change, but if FTDNA's Big Y matches thingy improves, that at least will be something. It hasn't been very good up until now.

simdadams
10-31-2017, 03:13 PM
My Big-y reprocess has complted , still shows MC21 and no matches as yet.

rms2
11-02-2017, 12:50 AM
My Big-y reprocess has complted , still shows MC21 and no matches as yet.

Did you have any matches before the big switcheroo? If so, then we're just waiting for them to get their updated Big Y results.

I'm still waiting for the one other guy at my terminal SNP (likely my 5th cousin) to get his updated Big Y results. In the meantime, it seems to me FTDNA's new Big Y matching system is light years ahead of the old one. My matches (back one and two steps upstream) are actual matches and not just a motley crew of nearly everyone in R1b Land like it was before.

JMcB
11-02-2017, 03:34 AM
I think we’re going to have to wait this one out for a while.

They initially finished my transfer quickly but I only had one match, as opposed to 51 before. However, he was the closest match I have. Then I gradually made my way up to four matches and they were all correctly placed on my SNP tree. So things were looking good.

Then a few days ago, they took them all away and I now have 0 matches. Which is surprising because I know all four of those matches have finished being updated.

simdadams
11-02-2017, 03:32 PM
Did you have any matches before the big switcheroo? If so, then we're just waiting for them to get their updated Big Y results.

I'm still waiting for the one other guy at my terminal SNP (likely my 5th cousin) to get his updated Big Y results. In the meantime, it seems to me FTDNA's new Big Y matching system is light years ahead of the old one. My matches (back one and two steps upstream) are actual matches and not just a motley crew of nearly everyone in R1b Land like it was before.

Yes I had matches before , from what you say it sounds a big improvement , thanks

R.Rocca
11-02-2017, 04:22 PM
Did you have any matches before the big switcheroo? If so, then we're just waiting for them to get their updated Big Y results.

I'm still waiting for the one other guy at my terminal SNP (likely my 5th cousin) to get his updated Big Y results. In the meantime, it seems to me FTDNA's new Big Y matching system is light years ahead of the old one. My matches (back one and two steps upstream) are actual matches and not just a motley crew of nearly everyone in R1b Land like it was before.

I have been very disappointed in the matching. There are two kits in my group that should show matches but do not, not even three or four levels up. The only matches I have seen is between kits that have family SNPs.

Cofgene
11-02-2017, 05:34 PM
I have been very disappointed in the matching. There are two kits in my group that should show matches but do not, not even three or four levels up. The only matches I have seen is between kits that have family SNPs.

Overall I think that is what is best in the long term. Matches several levels up goes to far back in time to be genealogically relevant. That was part of the problem with the old system. Having few or no matches drives the decision of getting extended family members and "close" STR matches to do the test to flesh out the structure closer to modern times.

R.Rocca
11-02-2017, 05:58 PM
Overall I think that is what is best in the long term. Matches several levels up goes to far back in time to be genealogically relevant. That was part of the problem with the old system. Having few or no matches drives the decision of getting extended family members and "close" STR matches to do the test to flesh out the structure closer to modern times.

I strongly disagree. There are many (most people that post on this forum) that want to trace their matches back to the pre-surname era. The old system showed matched based on the number of SNPs and this often fell back on the quality of the sample. It did not take into account matches on the tree.

Osiris
11-02-2017, 06:28 PM
I can't believe that all matches are showing for all members who completed the Big Y conversion yet.

Although on the other hand I have one completed kit in R-DF27 and one in R-U152. I can't imagine they'd list under the DF27 on the matching screen all Big Y testers who are DF27 xZZ12_1, that would be a huge list! For my other kit I'd have all U152 xL2 and L2 xA6454 which will also be massive. But then you'd think they'd have to because that's how I actually match them and that's where we'll learn the most by looking at the novel variants.

So maybe they just haven't loaded all matches yet from completed kits? I hope.

Cofgene
11-02-2017, 09:19 PM
I strongly disagree. There are many (most people that post on this forum) that want to trace their matches back to the pre-surname era. The old system showed matched based on the number of SNPs and this often fell back on the quality of the sample. It did not take into account matches on the tree.

The old system was completely clueless to the phylogeny of the tree when providing matches. My statement is still very valid in that the majority of individuals have haplogroup designations whose age is pre-surname. If FTDNA were to add ages to clades then allowing an individual to set an age-based matching level could make sense. But setting matches based upon a number of upstream branches will provide significant noise for the less educated customer - who are the majority.

R.Rocca
11-02-2017, 10:30 PM
The old system was completely clueless to the phylogeny of the tree when providing matches. My statement is still very valid in that the majority of individuals have haplogroup designations whose age is pre-surname. If FTDNA were to add ages to clades then allowing an individual to set an age-based matching level could make sense. But setting matches based upon a number of upstream branches will provide significant noise for the less educated customer - who are the majority.

I'm talking about 2 or three matches on the terminal branch, an additional 5 people one level above that, and 10 people above that. None of these matches are showing. I'm not talking about hundreds of phylogenetically irrelevant SNPs.

DillonResearcher
11-02-2017, 10:36 PM
My new Big Y results came through on the 25th and showed one match on that day I think but since then I have had none. The matching system also seems to suggest that I am the only U152 Big Y tester and there are certainly plenty of other U152 hg38 results about.

Hopefully it's just a case of being patient.

rms2
11-04-2017, 02:12 PM
I have been very disappointed in the matching. There are two kits in my group that should show matches but do not, not even three or four levels up. The only matches I have seen is between kits that have family SNPs.

Apparently the effort is patchy right now. Thus far for me the new thing is better. I did not at all like the old Big Y matching system, which I thought was worse than useless, since I had project members emailing me all the time asking me about "matches" who weren't even derived for the last four or five levels of SNPs that they were. It also had real matches buried further back than faux matches. That in part is what made YFull, Alex Williamson and do-it-yourself the only games in town.

rms2
11-04-2017, 03:41 PM
Here is something curious, but maybe only because of my own lack of knowledge.

According to FTDNA, I am derived for BY26207, which is a SNP I do not share with the matches with my surname one step back at FGC36974. YFull says BY26207 is not in its database, so I took a look at FTDNA's Y Chromosome Browser (nice feature) and found that BY26207 is position 11333103. I have a G there, and the reference allele is C.

When I checked for 11333103 at YFull, they said it was a "no call position". Yet, according to FTDNA the confidence level for me at BY26207 is "high".

So, what gives? Is FTDNA's revamped HG38 reference sequence yielding up stuff that wasn't showing up under HG19?

lgmayka
11-05-2017, 01:15 PM
When I checked for 11333103 at YFull, they said it was a "no call position".
Right now, YFull's Browse Raw Data only accepts an hg19 position, not an hg38 position. Did you remember to convert FTDNA's cited location to hg19 ?

rms2
11-05-2017, 01:40 PM
Right now, YFull's Browse Raw Data only accepts an hg19 position, not an hg38 position. Did you remember to convert FTDNA's cited location to hg19 ?

No, I did not. Thanks for the reminder. I'll try that.

Is there an easy-to-use method for doing that?

MacUalraig
11-05-2017, 02:10 PM
No, I did not. Thanks for the reminder. I'll try that.

Is there an easy-to-use method for doing that?

http://genome.ucsc.edu/cgi-bin/hgLiftOver

rms2
11-05-2017, 02:16 PM
http://genome.ucsc.edu/cgi-bin/hgLiftOver

I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.

Muircheartaigh
11-05-2017, 02:28 PM
I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.
Hg38 11333103 maps back to Hg19 13488779. However it is also present in the VCF files of my S841 group, sub group of Z253. And looking at the Hg19 BAM results it’s garbage with multiple Variants in the same read sequence. I’m seeing a lot of this type of result in the Hg38 reports in my group, and some of them have been given BY labels.

MacUalraig
11-05-2017, 02:32 PM
I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.

Just enter chrY:11333103-11333103 in the box labelled Paste in data and click Submit. Then double click where it says View conversions below.

rms2
11-05-2017, 02:34 PM
Just enter chrY:11333103-11333103 in the box labelled Paste in data and click Submit. Then double click where it says View conversions below.

Ah. I tried that but minus "chrY:" and the dash. Thanks. I'll give it another shot.

Muircheartaigh
11-05-2017, 02:40 PM
I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.

For a simple conversion try the NCBI Genome remapping service. You can input single locations, copy paste or upload files using the format Y.xxxxx-xxxxx in your case choose GrCh38(Hg38) as the source assembly and GrCh37(Hg19) as the target assembly and type Y.11333103-11333103 into the Data panel and submit

rms2
11-05-2017, 03:11 PM
Hg38 11333103 maps back to Hg19 13488779. However it is also present in the VCF files of my S841 group, sub group of Z253. And looking at the Hg19 BAM results it’s garbage with multiple Variants in the same read sequence. I’m seeing a lot of this type of result in the Hg38 reports in my group, and some of them have been given BY labels.

Thanks. Too bad. I was hoping this would be some new info that would be supported once the other guy with my terminal SNP (FGC36982) gets his updated Big Y results.

Muircheartaigh
11-05-2017, 03:35 PM
Thanks. Too bad. I was hoping this would be some new info that would be supported once the other guy with my terminal SNP (FGC36982) gets his updated Big Y results.

Here's an extract from the VCF file of a member of the S841 group that includes the location of BY26207 showing the reported values in the vicinity of the so called SNP IN question. This sort of garbage is appearing in some of the Hg38 results of members of my group and this is just the tip of the Iceberg. Two Members who share a common ancestor estimated at about 600 years ago have had their private SNPs increased from 5 in the Hg19 build to more than 20 in the Hg38 build. What is strange is that some of these garbage variants are being assigned ''BY'' labels.


11333005 A G,T
11333007 G C
11333009 G A
11333013 G A
11333028 T C
11333029 C A
11333032 G A
11333033 T G
11333037 G A
11333054 A G
11333057 G A
11333062 G A
11333067 C T
11333071 A G
11333079 C T
11333081 C T
11333096 G T
11333103 C G BY26207
11333116 C G
11333118 C A,G
11333119 G T
11333122 C A
11333128 C A
11333130 G A
11333131 G A
11333139 C G
11333140 G T
11333141 G T
11333143 C A,T
11333146 G C,A
11333152 T C
11333156 A T
11333157 G T
11333164 G A
11333166 T G
11333167 T C
11333168 G C
11333173 C T
11333174 G A
11333175 C T,A,G
11333176 G A
11333177 G T
11333179 G C
11333180 G A
11333186 C T
11333187 C A
11333189 G T
11333194 C T
11333195 G A,T,C

Cofgene
11-05-2017, 05:18 PM
Here's an extract from the VCF file of a member of the S841 group that includes the location of BY26207 showing the reported values in the vicinity of the so called SNP IN question. This sort of garbage is appearing in some of the Hg38 results of members of my group and this is just the tip of the Iceberg. Two Members who share a common ancestor estimated at about 600 years ago have had their private SNPs increased from 5 in the Hg19 build to more than 20 in the Hg38 build. What is strange is that some of these garbage variants are being assigned ''BY'' labels.


11333005 A G,T
11333007 G C
11333009 G A
11333013 G A
11333028 T C
11333029 C A
11333032 G A
11333033 T G
11333037 G A
11333054 A G
11333057 G A
11333062 G A
11333067 C T
11333071 A G
11333079 C T
11333081 C T
11333096 G T
11333103 C G BY26207
11333116 C G
11333118 C A,G
11333119 G T
11333122 C A
11333128 C A
11333130 G A
11333131 G A
11333139 C G
11333140 G T
11333141 G T
11333143 C A,T
11333146 G C,A
11333152 T C
11333156 A T
11333157 G T
11333164 G A
11333166 T G
11333167 T C
11333168 G C
11333173 C T
11333174 G A
11333175 C T,A,G
11333176 G A
11333177 G T
11333179 G C
11333180 G A
11333186 C T
11333187 C A
11333189 G T
11333194 C T
11333195 G A,T,C

All of us should be entering support tickets to FTDNA requesting that they stop naming inconsistent variants and PLEASE remove them from individuals lists of novel SNPs. They are creating the same type of mess as the original BigY analysis except it is worse with these automatic BY names being applied.

rms2
11-05-2017, 06:09 PM
Could it be some project admins are behind the rush to name unreliable variants? I don't mean they are picking unreliable SNPs on purpose, but in their excitement to get SNPs named perhaps they aren't being careful enough?

Muircheartaigh
11-05-2017, 07:01 PM
Could it be some project admins are behind the rush to name unreliable variants? I don't mean they are picking unreliable SNPs on purpose, but in their excitement to get SNPs named perhaps they aren't being careful enough?

Unlikely, this is a list from one of my group members' Known SNPS. The vast majority are garbage consecutively labelled from multiple variant sequences and I don't believe that any Admin, or anyone else for that matter would suggest labelling them as Valid. Obviously computer generated based in mis-aligned reads. Three of them are valid SNPs labelled just prior to the Hg19 to Hg38 upgrade.


BY26040 Yes (+) Yes G A High
BY26041 Yes (+) Yes C G High
BY26042 Yes (+) Yes C T High
BY26043 Yes (+) Yes C T High
BY26044 Yes (+) Yes C G High
BY26045 Yes (+) Yes T G High
BY26062 Yes (+) Yes G A High
BY26063 Yes (+) Yes A T High
BY26065 Yes (+) Yes T C High
BY26067 Yes (+) Yes T C High
BY26068 Yes (+) Yes G A High
BY26072 Yes (+) Yes T A High
BY26073 Yes (+) Yes G A High
BY26074 Yes (+) Yes T C High
BY26075 Yes (+) Yes G C High
BY26079 Yes (+) Yes A C High
BY26083 Yes (+) Yes C T High
BY26086 Yes (+) Yes A G High
BY26088 Yes (+) Yes T C High
BY26093 Yes (+) Yes T C High
BY26094 Yes (+) Yes C T High
BY26095 Yes (+) Yes G C High
BY26102 Yes (+) Yes T C High
BY26103 Yes (+) Yes T C High
BY26105 Yes (+) Yes T C High
BY26109 Yes (+) Yes C G High
BY26110 Yes (+) Yes T G High
BY26111 Yes (+) Yes A G High
BY26118 Yes (+) Yes A G High
BY26119 Yes (+) Yes T C High
BY26120 Yes (+) Yes G A High
BY26121 Yes (+) Yes T C High
BY26143 Yes (+) Yes A T High
BY26157 Yes (+) Yes G A High
BY26158 Yes (+) Yes A C High
BY26159 Yes (+) Yes A T High
BY26160 Yes (+) Yes T C High
BY26161 Yes (+) Yes T A High
BY26162 Yes (+) Yes C G High
BY26163 Yes (+) Yes G A High
BY26228 Yes (+) Yes T G High
BY26282 Yes (+) Yes C T High
BY26364 Yes (+) Yes A G High
BY26365 Yes (+) Yes G A High
BY26382 Yes (+) Yes A G High
BY26383 Yes (+) Yes G C High
BY26493 Yes (+) Yes A C High
BY26494 Yes (+) Yes A C High
BY26495 Yes (+) Yes T G High
BY26501 Yes (+) Yes C T High
BY26502 Yes (+) Yes G A High
BY26503 Yes (+) Yes C G High
BY26504 Yes (+) Yes A T High
BY26716 Yes (+) Yes C A High
BY26720 Yes (+) Yes T C High
BY26721 Yes (+) Yes A G High
BY26723 Yes (+) Yes G C High
BY26725 Yes (+) Yes A T High
BY26727 Yes (+) Yes A C High
BY26729 Yes (+) Yes T G High
BY26730 Yes (+) Yes C A High
BY26731 Yes (+) Yes C T High
BY26732 Yes (+) Yes T C High
BY26734 Yes (+) Yes T C High
BY26735 Yes (+) Yes T C High
BY26750 Yes (+) Yes T G High
BY26751 Yes (+) Yes T A High
BY26758 Yes (+) Yes T C High
BY26760 Yes (+) Yes T G High
BY26763 Yes (+) Yes C A High
BY26765 Yes (+) Yes G A High
BY26789 Yes (+) Yes G A High
BY26790 Yes (+) Yes A G High
BY26791 Yes (+) Yes A T High
BY26799 Yes (+) Yes T C High
BY26800 Yes (+) Yes G C High
BY26801 Yes (+) Yes A G High
BY26803 Yes (+) Yes C T High
BY26804 Yes (+) Yes G A High
BY26810 Yes (+) Yes C T High
BY26811 Yes (+) Yes G C High
BY26812 Yes (+) Yes T G High
BY26813 Yes (+) Yes C T High
BY26814 Yes (+) Yes G C High
BY26815 Yes (+) Yes T C High
BY26816 Yes (+) Yes T C High
BY26818 Yes (+) Yes G C High
BY26820 Yes (+) Yes T C High
BY26821 Yes (+) Yes G T High
BY26823 Yes (+) Yes C T High
BY26824 Yes (+) Yes C T High
BY26825 Yes (+) Yes G C High
BY26826 Yes (+) Yes A C High
BY26831 Yes (+) Yes G C High
BY26832 Yes (+) Yes G T High
BY26833 Yes (+) Yes A C High
BY26837 Yes (+) Yes A C High
BY26838 Yes (+) Yes G A High
BY26840 Yes (+) Yes A C High
BY26841 Yes (+) Yes C A High
BY26844 Yes (+) Yes A C High
BY26845 Yes (+) Yes C A High
BY26848 Yes (+) Yes T C High
BY26854 Yes (+) Yes G T High
BY26863 Yes (+) Yes A G High
BY26878 Yes (+) Yes G A High
BY26881 Yes (+) Yes A C High
BY26900 Yes (+) Yes T G High
BY26901 Yes (+) Yes G C High
BY26902 Yes (+) Yes A G High
BY26903 Yes (+) Yes T C High
BY26904 Yes (+) Yes A G High
BY26906 Yes (+) Yes C G High
BY26910 Yes (+) Yes A G High
BY26929 Yes (+) Yes T C High
BY26930 Yes (+) Yes C A High
BY26957 Yes (+) Yes A C High
BY26994 Yes (+) Yes C T High
BY26996 Yes (+) Yes G C High
BY27035 Yes (+) Yes T G High
BY27036 Yes (+) Yes A C High
BY27115 Yes (+) Yes T G High
BY27124 Yes (+) Yes C A High
BY27125 Yes (+) Yes C G High
BY27126 Yes (+) Yes G C High
BY27127 Yes (+) Yes G C High
BY27761 Yes (+) Yes A A High
BY27889 Yes (+) Yes T A High
BY28646 Yes (+) Yes C A High (VALID SNP)
BY28647 Yes (+) Yes G C High (VALID SNP)
BY28648 Yes (+) Yes A G High (VALID SNP)
BY28650 Yes (+) Yes G A High
BY28651 Yes (+) Yes C T High
BY28652 Yes (+) Yes T A High
BY28653 Yes (+) Yes G A High
BY28672 Yes (+) Yes C G High
BY28673 Yes (+) Yes C T High
BY28674 Yes (+) Yes A G High
BY28675 Yes (+) Yes T A High
BY28682 Yes (+) Yes C T High
BY28683 Yes (+) Yes A T High
BY28684 Yes (+) Yes C G High
BY28687 Yes (+) Yes A G High
BY28688 Yes (+) Yes A C High
BY28689 Yes (+) Yes G C High
BY28690 Yes (+) Yes A G High
BY28691 Yes (+) Yes T G High
BY28693 Yes (+) Yes G A High
BY28695 Yes (+) Yes C A High
BY28700 Yes (+) Yes A G High
BY28701 Yes (+) Yes C T High
BY28702 Yes (+) Yes C A High
BY28703 Yes (+) Yes C A High
BY28704 Yes (+) Yes T C High
BY28705 Yes (+) Yes A G High
BY28706 Yes (+) Yes C G High
BY28707 Yes (+) Yes C T High
BY28708 Yes (+) Yes T G High
BY28709 Yes (+) Yes C T High
BY28710 Yes (+) Yes G C High
BY28711 Yes (+) Yes G C High
BY28712 Yes (+) Yes C G High
BY28713 Yes (+) Yes T G High
BY28716 Yes (+) Yes C T High
BY28717 Yes (+) Yes C T High
BY28718 Yes (+) Yes C T High
BY28719 Yes (+) Yes C T High
BY28722 Yes (+) Yes G A High
BY28723 Yes (+) Yes G C High
BY28726 Yes (+) Yes A T High
BY28728 Yes (+) Yes C A High
BY28729 Yes (+) Yes G A High
BY28730 Yes (+) Yes T A High
BY28731 Yes (+) Yes T C High
BY28732 Yes (+) Yes T A High
BY28734 Yes (+) Yes C G High
BY28746 Yes (+) Yes G C High
BY28749 Yes (+) Yes A C High
BY28753 Yes (+) Yes C G High
BY28754 Yes (+) Yes G C High
BY28759 Yes (+) Yes A C High
BY28761 Yes (+) Yes A G High
BY28762 Yes (+) Yes G C High
BY28773 Yes (+) Yes T G High
BY28780 Yes (+) Yes A C High

simdadams
11-17-2017, 04:46 PM
I have lost any R-MC21 matches , I have two at l21 and two at DF13 , 0 at Z39589 and 0 at DF41 ?

L21 R-L21 2
DF13 R-DF13 2
Z39589 R-Z39589 0
DF41 R-DF41 0
MC21 R-MC21 YOU 0

rms2
11-18-2017, 12:33 AM
I have lost any R-MC21 matches , I have two at l21 and two at DF13 , 0 at Z39589 and 0 at DF41 ?

L21 R-L21 2
DF13 R-DF13 2
Z39589 R-Z39589 0
DF41 R-DF41 0
MC21 R-MC21 YOU 0

You're probably just waiting for your MC21 matches to get their HG38 updates. I had the same experience until my likely 5th cousin got his updated Big Y results back.

simdadams
02-14-2018, 01:38 PM
Have yours been updated yet, nothing still on mine

Petr
02-14-2018, 09:11 PM
What do you see at https://www.familytreedna.com/my/awaiting-results.aspx ? Maybe FTDNA sent you a new kit? because of quality problems?

simdadams
02-15-2018, 09:33 AM
What do you see at https://www.familytreedna.com/my/awaiting-results.aspx ? Maybe FTDNA sent you a new kit? because of quality problems?

Nothing there, apart from an autosomnal transfer , hmmm

rms2
02-15-2018, 12:57 PM
Have yours been updated yet, nothing still on mine

I have fewer matches than before , but that's fine because the prior system was a mess. Now the matches I have are actually fairly close and make sense.