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Thread: FGC BAM file analysis

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    FGC BAM file analysis

    I was wondering if more SNPs would he discovered by uploading my FTDNA Big Y 700 raw bam files to Full Genomes. I was curious what this would accomplish and if it is worth me purchasing my raw bam files for 100 dollars and uploading them to Full Genomes for 50 dollars.
    Will any FGC SNPs discovered end up in the Y block tree on FTDNA? How does this work?

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    Probably it would discover some new SNPs, but many of these additional SNPs may be of questionable quality. You'll get a data output which can be opened in a spreadsheet such as excel which will provide FGC's rating for these. The report also provides a list of STRs they extract from the BAM and some of these will likely be different to those reported by FTDNA as well as INDELs - FGC seem to have the best handle on these compared to the other main commercial analysis companies.

    Analysis by FGC will make no difference to the FTDNA block tree. FTDNA only uses it's own results and analysis, although they have recently been adding ancient samples to their database.

    It's probably more useful in a deep dive of several similarly tested individuals on close branches as part of a project and less useful for a single individual.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by Murphy View Post
    I was wondering if more SNPs would he discovered by uploading my FTDNA Big Y 700 raw bam files to Full Genomes. I was curious what this would accomplish and if it is worth me purchasing my raw bam files for 100 dollars and uploading them to Full Genomes for 50 dollars.
    Will any FGC SNPs discovered end up in the Y block tree on FTDNA? How does this work?
    I will spend that 100+50=$150 on Dante Labs 30X WGS when on sale it usually costs $149 US.

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    If it doesn't make a difference to the Haplotree how do all the FGC and non BY and FT SNPs end up in the FTDNA block tree? Thank you!

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    Because they are discovered in NGS tests from other companies (FGC, YSEQ, Dante, etc.) or analysis by BAM analysis by the likes of FGC and YFull or Y-DNA project administrators, registered on YBrowse and then later found positive in Big Y customers where the results show these are positive for these SNPs. FTDNA is a lot more aggressive in calling Y-SNPs than they used to be in the earlier days of the Big Y.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    So it may be possible that if myself and some others transfer results to FGC or YFull that there may be more SNPs discovered? Would these potentially be tracked by Big Y if such an event occurs? I do recall an FGC marker being found much later between Z and FGC markers. Kind of strange considering it didn't split any branches, but just happened to be in-between

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    Quote Originally Posted by Murphy View Post
    So it may be possible that if myself and some others transfer results to FGC or YFull that there may be more SNPs discovered? Would these potentially be tracked by Big Y if such an event occurs? I do recall an FGC marker being found much later between Z and FGC markers. Kind of strange considering it didn't split any branches, but just happened to be in-between
    It’s possible. When I submitted my results to YFull they found a Novel Variant in the combBED that I later used in my SNP Pack at YSEQ. When my three closest matches upgraded to Y700, they all matched the SNP in question. For some reason Family Tree didn’t listed it, even though at least four people were positive for the SNP. When I search for it in our results at Family Tree, I couldn’t find it anywhere. To Family Tree’s credit, when I called them up and ask why it wasn’t listed as one of our branches Terminal SNPs, they took a look and then added it to our block of SNPs. Sometimes things can fall through the cracks. Although, I suspect it doesn’t happen all that often.
    Last edited by JMcB; 05-24-2021 at 02:46 AM.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Sicilian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Sicilian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegean 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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    FTDNA is acting extremely aggressive and dismissive towards orgs like YFULL.

    I've experienced it myself, especially with the latest Turkish study and the publication of the relevant .CRAMS, which will, in many cases, massively transform the branching in certain clades.

    The drama and sour grapes from the admins and users alike of the BigY crowd is unreal.
    dosas: 56.25% Greek_Macedonia + 43.75% Greek_Trabzon @ 1.769
    wife: 50% English + 50% Irish @ 1.837
    kid1: 56.25% English + 43.75% Greek_Cappadocia @ 1.817
    kid2: 56.25% English_Cornwall + 43.75% Greek_Cappadocia @ 1.866

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    I wonder if they would actually take the time to do test the SNPs further downstream that are assumed positive. There is a group of O'Sheas of NW Cork and some Foleys that share the upstream mutation BY582 which has several variants that may change how long ago we broke off into separate families.
    In my current position I am fortunate with the number of Murphys who have tested, the number of them with known NPEs, Big Y results, etc.

    As a co-administrator I sometimes see pending lab results for those with big Y results finalized that state a Y Haplogroup Backbone. Some of them are estimated to be finished several months ago. Not sure what this could mean in terms of updates. I would like to be able to get more people to test SNPs and private variants among our members downstream of BY582 instead of having to purchase a Big Y.

    I think it is likely we sprung out of Muskerry around the 13th century.

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    Quote Originally Posted by Murphy View Post
    I wonder if they would actually take the time to do test the SNPs further downstream that are assumed positive. There is a group of O'Sheas of NW Cork and some Foleys that share the upstream mutation BY582 which has several variants that may change how long ago we broke off into separate families.
    In my current position I am fortunate with the number of Murphys who have tested, the number of them with known NPEs, Big Y results, etc.

    As a co-administrator I sometimes see pending lab results for those with big Y results finalized that state a Y Haplogroup Backbone. Some of them are estimated to be finished several months ago. Not sure what this could mean in terms of updates. I would like to be able to get more people to test SNPs and private variants among our members downstream of BY582 instead of having to purchase a Big Y.

    I think it is likely we sprung out of Muskerry around the 13th century.
    You can use YSEQ for testing individual SNPs or for constructing your own SNP Pack. I made one for nine of my Novel Variants and used it to test two different matches at one point. It’s fairly easy to do and cheaper in most cases. Although, to be honest, I would rather have them upgrade to Y700, if they’re already in Family Tree’s system.
    Last edited by JMcB; 05-24-2021 at 06:22 PM.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Sicilian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Sicilian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegean 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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