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Thread: Ancient I-M253 samples list

  1. #761
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    Quote Originally Posted by romelson View Post
    Are you using samtools for analyzing the VK BAM files?
    I just installed samtools in Ubuntu and downloaded a couple of VK BAM-files to have look if I can figure further haplogroup designation for some of the I1 samples.
    I am well familiar with BigY:s, Y-haplotrees, private SNPs and administrate several projects at FTDNA.
    But have never used samtools before. Is there some good tutorial for how to go about next to analyze the BAM files?

    I’m using this website:


    https://www.ncbi.nlm.nih.gov/project...srz=ERR4059742

    Instead of “ERR4059742” put in the label of your particular Viking Study sample which can be found at this website:

    https://www.ebi.ac.uk/ena/browser/view/PRJEB37976

    In the tab that says “Find” put in the Hg19 base pair location for the particular SNP you’re looking at. I used YFull to find the Hg19 locations but I heard Ybrowse works too.
    Haplogroup I, I1

    DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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  3. #762
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    Quote Originally Posted by mwauthy View Post
    Do you think YFull is doing this proactively for all the samples or are people contacting YFull regarding particular samples? Iím wondering if I should email them regarding VK446?
    I sent an email to YFull about the paper and a link to the BAM files but I think they were already well aware and likely taking action before that. If I was them, I would be working my way down the list from the highest coverage samples to the lowest. I don't believe that they are doing it individually by request per sample. However, there is no harm in emailing them and asking - they may tell you that the coverage isn't enough for a particular sample.

    I'd recommend letting the dust settle on this one. YFull are adding samples to their haplotree, but there will become a point when some samples won't get added because the coverage isn't good enough - see for example the ancient Icelanders paper from 2018 - of the six I1 samples, YFull added 3 to their tree (the ones with the best coverage) but left the three with the worst coverage off. After YFull have added all that they are going to add, we can pick the bones out of the remaining ones.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  5. #763
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    Quote Originally Posted by romelson View Post
    Are you using samtools for analyzing the VK BAM files?
    I just installed samtools in Ubuntu and downloaded a couple of VK BAM-files to have look if I can figure further haplogroup designation for some of the I1 samples.
    I am well familiar with BigY:s, Y-haplotrees, private SNPs and administrate several projects at FTDNA.
    But have never used samtools before. Is there some good tutorial for how to go about next to analyze the BAM files?
    I'm using IGV from the Broad Institute http://software.broadinstitute.org/software/igv/ Don't have any familiarity with samtools or linux/unix systems or Ubuntu. The Dante Labs and Nebula Genomics Customers Facebook group seems to have a few people who are into samtools, etc. so would try there for questions/tutorials.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by deadly77 View Post
    I sent an email to YFull about the paper and a link to the BAM files but I think they were already well aware and likely taking action before that. If I was them, I would be working my way down the list from the highest coverage samples to the lowest. I don't believe that they are doing it individually by request per sample. However, there is no harm in emailing them and asking - they may tell you that the coverage isn't enough for a particular sample.

    I'd recommend letting the dust settle on this one. YFull are adding samples to their haplotree, but there will become a point when some samples won't get added because the coverage isn't good enough - see for example the ancient Icelanders paper from 2018 - of the six I1 samples, YFull added 3 to their tree (the ones with the best coverage) but left the three with the worst coverage off. After YFull have added all that they are going to add, we can pick the bones out of the remaining ones.
    It’s nice to see they’re going up so quickly. Needless to say, it makes sense for them to add all that they can responsibly. Depending on the sample’s quality. As it’s a nice feature for their tree and I suspect their normal submissions have probably suffered because of the Bam file tax.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 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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    Quote Originally Posted by spruithean View Post
    I would be very wary of a 67 marker match, especially once it becomes quite close to being a low probability of a shared recent common ancestor. I say this because I have several 67 marker matches to individuals with ancestors who originated not too far from where my paternal lineage is believed to have come from. Initially, I would have assumed a recent connection, but Big Y testing has shown that the connection is much further back in time and definitely before the advent of surnames.

    I'm not sure who this Leofwine of Normandy fellow is? The name Leofwine is a rather Old English (Anglo-Saxon) given name, that I wouldn't expect to see in Normandy. Do the various genealogies for the Claytons have good sources and documentation back to this Leofwine?
    The info about Leofwine was posted by StoneMeadow last year (for which my thanks). It can be found at post #472 in this thread. I can't vouch for its authenticity but I have seen it online elsewhere in greater detail.

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    Quote Originally Posted by deadly77 View Post
    I sent an email to YFull about the paper and a link to the BAM files but I think they were already well aware and likely taking action before that. If I was them, I would be working my way down the list from the highest coverage samples to the lowest. I don't believe that they are doing it individually by request per sample. However, there is no harm in emailing them and asking - they may tell you that the coverage isn't enough for a particular sample.

    I'd recommend letting the dust settle on this one. YFull are adding samples to their haplotree, but there will become a point when some samples won't get added because the coverage isn't good enough - see for example the ancient Icelanders paper from 2018 - of the six I1 samples, YFull added 3 to their tree (the ones with the best coverage) but left the three with the worst coverage off. After YFull have added all that they are going to add, we can pick the bones out of the remaining ones.

    Yeah so far YFull have added 2/4 samples I was interested in (VK521 and VK496) to their Haplotree, and they both have the highest coverage of the 4 samples (4.538 and 1.978).

    I do hope though that they eventually add VK446 because it’s the closest to my direct patrilineal line, but the coverage is only 1.531. I’m not sure what their coverage cutoff will be? Anyhow, I went ahead and sent them an email about VK446 in case that helps?
    Haplogroup I, I1

    DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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  13. #767
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    Quote Originally Posted by JMcB View Post
    It’s nice to see they’re going up so quickly. Needless to say, it makes sense for them to add all that they can responsibly. Depending on the sample’s quality. As it’s a nice feature for their tree and I suspect their normal submissions have probably suffered because of the Bam file tax.
    It looks like FTDNA is also adding the samples from these studies to their tree - there's an in progress list here with some comments from FTDNA on some samples about how they split a phylogenetic block or match with a sample in their database https://dna-explained.com/2020/09/18...-updates-here/

    It wouldn't happen, and would be a little bit petty, but it would be amusing if European Nucleotide Archive decided to charge FTDNA $100 for each BAM file they downloaded from this study. Joking of course.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by mwauthy View Post
    Yeah so far YFull have added 2/4 samples I was interested in (VK521 and VK496) to their Haplotree, and they both have the highest coverage of the 4 samples (4.538 and 1.978).

    I do hope though that they eventually add VK446 because it’s the closest to my direct patrilineal line, but the coverage is only 1.531. I’m not sure what their coverage cutoff will be? Anyhow, I went ahead and sent them an email about VK446 in case that helps?
    No harm in asking - as they say in my part of the world "shy bairns get nowt".

    In an earlier post on this thread #442 https://anthrogenica.com/showthread....l=1#post585545 I put the I1 samples in order of coverage and mentioned some of the ones that made it on to the YFull tree for comparison. I guess we will see when YFull completes - might take a few days since there are a lot of samples to get through.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  17. #769
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    Quote Originally Posted by deadly77 View Post
    No harm in asking - as they say in my part of the world "shy bairns get nowt".

    In an earlier post on this thread #442 https://anthrogenica.com/showthread....l=1#post585545 I put the I1 samples in order of coverage and mentioned some of the ones that made it on to the YFull tree for comparison. I guess we will see when YFull completes - might take a few days since there are a lot of samples to get through.

    VK446 was finally added to the YFull Haplotree at subclade branch I-FGC24357 so I’m a happy man. They even made a note that this sample could hypothetically even be positive all the way down to I-Y125947 on my direct patrilineal line because a lot of the downstream SNPs weren’t even covered on the test.
    Haplogroup I, I1

    DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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    Quote Originally Posted by deadly77 View Post
    It looks like FTDNA is also adding the samples from these studies to their tree - there's an in progress list here with some comments from FTDNA on some samples about how they split a phylogenetic block or match with a sample in their database https://dna-explained.com/2020/09/18...-updates-here/

    It wouldn't happen, and would be a little bit petty, but it would be amusing if European Nucleotide Archive decided to charge FTDNA $100 for each BAM file they downloaded from this study. Joking of course.
    While perhaps petty, it would also be poetic justice but it won’t happen. Perhaps, I misunderstood the article but from my understanding they aren’t actually putting the VK samples on their tree, their using them to make any appropriate changes they come across. Which you can look for in the article as she updates it. So for example, a new branch formed with a modern person, will show that person but not the VK sample. On one of the FB pages Tiger Walsh said he was trying to get them to actually list the samples but I don’t know where that stands at this point.
    Last edited by JMcB; 09-18-2020 at 08:23 PM.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 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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