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Thread: YFull updates

  1. #1
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    YFull updates

    I'm starting this as a general thread on YFull updates.
    https://www.yfull.com/

    I'm fine with the moderators moving this to the Commercial category but YFull does not have its own sub-category there so I'll open it here and let the moderators decide if it should be moved.

    YFull interprets Next Generation Sequencing BAM files and provides services that you need to be fairly technical to do themselves. They also provide a tree and group administration for various subclades on the three.

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    I've been asking for a "re-interpretation" fee for Big Y (FTDNA) NGS testers who are also YFull interpretation service customers. I doubt if they are responding directly to my request but they probably have multiple customers with interest in this.

    Big Y results are in the process of being upgraded to the Hg38 reference which means new Hg38 based BAM files will be available.

    YFull has responded with how they will support this. I just saw this.
    https://www.yfull.com/static/hg38.html

    Quote Originally Posted by YFull
    We have been busy planning on how to respond to recent hg38/GRCh38 developments and have been working on complex and deep algorithm improvements for the YFull system. We apologize for not having communicated about this sooner.

    The algorithm improvements are intended to allow us to simultaneous work in any build, including hg19/CRCh37, hg38/GRCh38 as well as new assemblies that may appear in the future (for example hg39, hg40 etc.).

    Our YFull service will continue working and accepting only NEW orders and .BAM files regardless of build type, both in hg19/GRCh37 and hg38/GRCh38, and the program will automatically determine the assembly and required genome reference. During the algorithm improvement development, our service will be in a transition period. Recently we temporarily added positions to hg38 on the page "Novel SNPs" as additional information. After the transition period, for samples already analyzed in hg19, you will have the option to select the display of items on the "Novel SNPs" page by switching between hg19/hg38. This will be implemented as part of the "select" process for accounts with multiple samples, and as link-buttons for accounts with one sample. Similar interface upgrades will also be added to the Groups and other service pages for your easy use.

    Many people have been discussing hg38, and have been wondering if whether additional information can be extracted from the raw data. There are various pros and cons and in general we think many people may be disappointed. Yes, indeed, the new build includes a lot of changes, mainly due to autosomal chromosomes. Surprisingly, the total length of the Y-chromosome in the new build decreased by 2 million base pairs and became shorter. Many "new" regions were added near the centromere, and because of common problems with mapping these regions, additional "trash" appeared in the form of unreliable and false variants. This also adds problems with filtering such variants. And some small segments in the DYZ19 region were, on the contrary, excluded from the sequence.
    ....
    Nevertheless, we suspect that some users of our service my still want to upgrade the raw data mapped in hg38 in order to get new variants. We want to provide this opportunity to you. And for this case we developing an additional service "Hg38 upgrade" at cost of $15. This analysis is NOT NECESSARY! The service will be available after being tested with a new .BAM file mapped at hg38 and when we make sure it works correctly.
    Good news, they do have a reduced or discounted "upgrade" fee of only $15. I haven't studied this but this is start into the topic.

    Please let us focus on YFull on this. They will perform interpretations of FGC, FTDNA, and (I think) YSEQ NGS and WGS test results but if you want to delve into those testing institutions beyond stuff that is directly YFull related I suggest creating topics under those vendor sub-categories.
    Last edited by TigerMW; 10-27-2017 at 04:03 PM.

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    'Using the wrong form to order the Hg38 upgrade will introduce considerable disorder and create a duplicate in the database! '

    Oh goody, I submitted my Full Genomes hg38 BAM yesterday on the standard form.

    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
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    Quote Originally Posted by Mikewww View Post
    I've been asking for a "re-interpretation" fee for Big Y (FTDNA) NGS testers ...

    Big Y results are in the process of being upgraded to the Hg38 reference which means new Hg38 based BAM files will be available.

    YFull has responded with how they will support this. I just saw this.
    https://www.yfull.com/static/hg38.html
    It seems like YFull is pooh-poohing Hg38 a bit. They are making what I think is a great offer, a re-interpretation for only $15 bu then they go on to emphasize in all capital letters this is "NOT NECESSARY".

    Quote Originally Posted by YFull
    We want to provide this opportunity to you. And for this case we developing an additional service "Hg38 upgrade" at cost of $15. This analysis is NOT NECESSARY!
    Interpretation services in and of themselves are not necessary. You can work with free BAM utilities and do it yourself and we see many project admins can help but I like the idea of having a professional opinion. Maybe I'm misreading this but you would think they would want to encourage the submission of true Hg38 BAM files. Granted, some variants may be gone but the whole idea of Hg38 mapping is it much better so we we also get new variants and get far better quality in the calls. No?

    The idea of an interpretation services is to get the most out of your NGS test. If so, why not use a better reference, Hg38?
    Last edited by TigerMW; 10-27-2017 at 09:39 PM.

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    Quote Originally Posted by Mikewww View Post
    It seems like YFull is pooh-poohing Hg38 a bit. They are making what I think is a great offer, a re-interpretation for only $15 bu then they go on to emphasize in all capital letters this is "NOT NECESSARY".



    Interpretation services in and of themselves are not necessary. You can work with free BAM utilities and do it yourself and we see many project admins can help but I like the idea of having a professional opinion. Maybe I'm misreading this but you would think they would want to encourage the submission of true Hg38 BAM files. Granted, some variants may be gone but the whole idea of Hg38 mapping is it much better so we we also get new variants and get far better quality in the calls. No?

    The idea of an interpretation services is to get the most out of your NGS test. If so, why not use a better reference, Hg38?
    what Yfull mean to say is that they where ahead of BigY ( like for me ) and it is not necessary because they have already found the SNP's that the BigY upgrade are finding.

    ..........How many will be disappointed if they paid their $15 and fell in the "not necessary" group ! ..........one needs to determine where they stand once Bigy is completed.

    For me , I do not need it , I have my SNP , ftdna Bigy has caught up to Yfull , plus my private SNP will be upgrade to a new branch if others are found to have it.......meaning it will no longer be private ............but this is in the future


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483 )


    Grandfather via paternal grandmother = I1-L22 ydna
    Great grandmother paternal side = T1a1e mtdna

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    Quote Originally Posted by vettor View Post
    what Yfull mean to say is that they where ahead of BigY ( like for me ) and it is not necessary because they have already found the SNP's that the BigY upgrade are finding.
    There is no magic in finding SNPs in Big Y BAM files. FGC does it too as well as many project admins. FTDNA's Michael Sager even does it when needed to analyze adding a branch to the tree. It's just that Big Y's automated calling system was too strict. YFull can't be ahead of Big Y where they are using Big Y as the source. Their interpretations can be advanced over FTDNA's interpretations, though, particularly FTDNA's automated test caller.

    Do you understand that the Hg38 map is different and there may be variants not in the old Hg19 BAM files in the YFull database? The improving mapping enables coverage of some previously not referenced locations. In addition, the improved mapping of Hg38 improves the confidence of calls.

    Why not take advantage of it? It's up to everyone to do what they want but for $15 it seems like easy deal to accept.

    YFull will miss SNPs that the improving Hg38 mapping will allow that are in the old Hg19 BAM files. They have also called some variants of low quality that they could see in the new Hg38 BAMs were clearly not being valid in the first place. However, if we resubmit they will get the new information. That doesn't mean they have to throw away the old Hg19 files.
    Last edited by TigerMW; 10-27-2017 at 10:22 PM.

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    Quote Originally Posted by Mikewww View Post
    There is no magic in finding SNPs in Big Y BAM files. FGC does it too as well as many project admins. FTDNA's Michael Sager even does it when needed to analyze adding a branch to the tree. It's just that Big Y's automated calling system was too strict. YFull can't be ahead of Big Y where they are using Big Y as the source. Their interpretations can be advanced over FTDNA's interpretations, though, particularly FTDNA's automated test caller.

    Do you understand that the Hg38 map is different and there may be variants not in the old Hg19 BAM files in the YFull database? The improving mapping enables coverage of some previously not referenced locations. In addition, the improved mapping of Hg38 improves the confidence of calls.

    Why not take advantage of it? It's up to everyone to do what they want but for $15 it seems like easy deal to accept.

    YFull will miss SNPs that the improving Hg38 mapping will allow that are in the old Hg19 BAM files. They have also called some variants of low quality that they could see in the new Hg38 BAMs were clearly not being valid in the first place. However, if we resubmit they will get the new information. That doesn't mean they have to throw away the old Hg19 files.
    I have no problem with what you say and also, $15 is no big deal, I will also go down this hg38 line , but I am prepared to receive nothing additional.

    I never had a Yfull match and the old BigY I had 3 matches ( which I contacted all 3 people ) but they seem to be about 9 plus generations away from me, I currently have zero matches in the new BigY ........so, I have nothing to loose in paying the $15 to yfull


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483 )


    Grandfather via paternal grandmother = I1-L22 ydna
    Great grandmother paternal side = T1a1e mtdna

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    Quote Originally Posted by Mikewww View Post
    YFull will miss SNPs that the improving Hg38 mapping will allow that are in the old Hg19 BAM files.
    The question is whether the conversion of a BAM file from hg19 to hg38 offers any practical value to a Big Y customer. You quote YFull thus:
    ---
    Many people have been discussing hg38, and have been wondering if whether additional information can be extracted from the raw data. There are various pros and cons and in general we think many people may be disappointed. Yes, indeed, the new build includes a lot of changes, mainly due to autosomal chromosomes. Surprisingly, the total length of the Y-chromosome in the new build decreased by 2 million base pairs and became shorter. Many "new" regions were added near the centromere, and because of common problems with mapping these regions, additional "trash" appeared in the form of unreliable and false variants. This also adds problems with filtering such variants. And some small segments in the DYZ19 region were, on the contrary, excluded from the sequence.
    ---

    Since I am retired on a fixed income, I myself cannot afford to spend $15 per YFull entry in my custody unless/until others actually report significant value in the hg19-to-hg38 conversion. We shall see.

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    Quote Originally Posted by lgmayka View Post
    The question is whether the conversion of a BAM file from hg19 to hg38 offers any practical value to a Big Y customer. You quote YFull thus:
    ---
    Many people have been discussing hg38, and have been wondering if whether additional information can be extracted from the raw data. There are various pros and cons and in general we think many people may be disappointed. Yes, indeed, the new build includes a lot of changes, mainly due to autosomal chromosomes. Surprisingly, the total length of the Y-chromosome in the new build decreased by 2 million base pairs and became shorter. Many "new" regions were added near the centromere, and because of common problems with mapping these regions, additional "trash" appeared in the form of unreliable and false variants. This also adds problems with filtering such variants. And some small segments in the DYZ19 region were, on the contrary, excluded from the sequence.
    ---

    Since I am retired on a fixed income, I myself cannot afford to spend $15 per YFull entry in my custody unless/until others actually report significant value in the hg19-to-hg38 conversion. We shall see.
    Yes that is the pooh-poohing. Scientists produced Hg38 as the 38th attempt of a reference model for human genome. It seems like we would want to leverage the improvements.

    I understand. There is nothing wrong with wait and see. How many BAM files do you need to upgrade? I only have two today but hope to have another soon. You might part with $15 on your personal paternal lineage BAM and see how it goes.

    It is funny that the biggest YFull advocate I know has been skewering folks (another forum) because the only correct way to do this is to back to the FASTQ files and re-create and re-analyze true Hg38 BAMs. I told him we should ask what YFull wants. We are getting better idea of what they want.
    Last edited by TigerMW; 10-28-2017 at 12:43 AM.

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    Quote Originally Posted by Tomenable View Post
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    Maybe you belong to some yet unknown branch of R-L617

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