Announcement

Collapse
No announcement yet.

Well, so much for that...

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Kathleen Carrow
    replied
    Originally posted by Rebekah Canada View Post
    Hi,

    I know that Felix has been working on a Y-Merge tool.
    http://www.y-str.org/2014/04/merge-y.html
    I am sure he would appreciate feedback on how it works and what else the community would like to see.
    Rebekah
    This was an important post and thanks.. I have quoted it to my own folks..

    Leave a comment:


  • MitchellSince1893
    replied
    Thanks...opening with excel didn't work until I opened excel first and navigated to the bed location (as opposed to clicking on bed file and selecting excel as the program to open the bed file with).

    Leave a comment:


  • dtvmcdonald
    replied
    bed and vcf files are human readable as-is.

    I use Excel, but any text editor will do too.

    Bam needs special tools and auxiliary files.

    Doug McDonald

    Leave a comment:


  • MitchellSince1893
    replied
    Originally posted by dtvmcdonald View Post
    You can tell between no-calls and ancestral with just
    the bed and vcf files. If it is not in the bed file its
    a no-call. If its in the bed but not the vcf its not
    a relible derived. Its probably ancestral, but if a look
    in the vcf files indicates its in the region of lots of no-calls it might be heterozygous. You might want to look at the bam file to be absolutely sure if its really important.
    What program are you using to view the bed files?

    Leave a comment:


  • dtvmcdonald
    replied
    Originally posted by lgmayka View Post
    You can do that if you have multiple Big Y results (from the same clade) with which to compare. But even then, you may encounter one major handicap:

    For the Known SNPs, you can distinguish between derived, ancestral, and no-call. But for Novel Variants, you cannot distinguish between ancestral vs. no-call except via the BAM file.

    For a very limited time, Full Genomes is also (like YFull) interpreting BAM files at no charge.
    You can tell between no-calls and ancestral with just
    the bed and vcf files. If it is not in the bed file its
    a no-call. If its in the bed but not the vcf its not
    a relible derived. Its probably ancestral, but if a look
    in the vcf files indicates its in the region of lots of no-calls it might be heterozygous. You might want to look at the bam file to be absolutely sure if its really important.

    Leave a comment:


  • DeeTyler
    replied
    Bearing in mind that I am a relative rookie in all this, take this with a grain of salt. Based on what I see in my results and muddling through the various posts at Molgen, it appears as though we might fit in as another branch off of FG1228.

    But beyond that I haven't a clue. 8-)

    Leave a comment:


  • muso
    replied
    Originally posted by DeeTyler View Post
    Thank you muso, I have been in frequent contact with Larry Mayka, who is also part of the R1a project (we're already there). He's got me covered and he has more than my blessings to use it to further the project knowledge. That was the main reason I ordered it. 8-)

    I also received a notice from FTDNA to acknowledge the request for the BAM file but it might take up to a couple of weeks. I am planning to upload it to YFull as soon as I get it!

    EDIT ... is Lukasz in the forums at Molgen? I was pointed to a thread there and signed up so that I could post, but this is the third time I've tried, and I seem not to get the emails to confirm my email address. If that's the case, then perhaps I can just email Lukasz directly and have him share some of our results. I did notice that we are already included on some of the R1a diagrams but now some of those "unknowns" relating to us are known and we can fill out that tree a little more. ;-)
    He is there, on the English site. I look forward to seeing where you fit on the updated tree.

    Leave a comment:


  • DeeTyler
    replied
    Thank you muso, I have been in frequent contact with Larry Mayka, who is also part of the R1a project (we're already there). He's got me covered and he has more than my blessings to use it to further the project knowledge. That was the main reason I ordered it. 8-)

    I also received a notice from FTDNA to acknowledge the request for the BAM file but it might take up to a couple of weeks. I am planning to upload it to YFull as soon as I get it!

    EDIT ... is Lukasz in the forums at Molgen? I was pointed to a thread there and signed up so that I could post, but this is the third time I've tried, and I seem not to get the emails to confirm my email address. If that's the case, then perhaps I can just email Lukasz directly and have him share some of our results. I did notice that we are already included on some of the R1a diagrams but now some of those "unknowns" relating to us are known and we can fill out that tree a little more. ;-)
    Last edited by DeeTyler; 3 April 2014, 05:34 PM.

    Leave a comment:


  • muso
    replied
    Originally posted by DeeTyler View Post
    I was just looking at this, it's very slick!

    It accurately found our group (R1a-L1029), but in addition to that the Morley DNA page listed a whole slew of SNPs that were not accounted for in that designation. Over 300 of them from the looks of it.

    Is there any place that might provide more information about the SNPs on that "unaccounted for" list?

    (Still waiting for the BAM file download)
    Submit your BAM file to YFull, my fellow L1029 member! You will get plenty of further analysis. Also, please give permission to Łukasz Łapiński ([email protected]) , Group Administrator at the R1a Project, to share your SNPs for the sake of comparison. If you need a contact for YFull, PM me and I will provide it to you.

    Leave a comment:


  • dtvmcdonald
    replied
    But what's the current estimate of ALL the snps
    found by BigY? (in years)?

    What's the estimate for new, real, indels?

    For the SNPs I'm finding it looks a lot more like 100
    or 120 years. But that may include unreliable ones.
    It does not include the ones FTDNA marks fail.

    Doug McDonald

    Leave a comment:


  • lgmayka
    replied
    Originally posted by Earl Davis View Post
    For any else looking for more immediate analysis of results Roberta Estes has provided an overview of of very own Felixs' Chrome extension that can help you get more from your results.

    http://dna-explained.com/2014/04/02/...ome-extension/
    Unfortunately, that tool only works for the customer himself, not for project administrators. It did work for administrators at one time, but no longer.

    Leave a comment:


  • lgmayka
    replied
    Originally posted by Earl Davis View Post
    Of course the rate at which new SNP's occur will come under heavy debate as BIgY results continue to be analysed and new people test so I am in no way saying that 3 will ultimately be correct figure but it seems to be what several people are currently thinking.
    The best estimate I've seen recently is that the Big Y finds one reliable SNP per 165 years of history. Keep in mind that:
    - The Big Y is not as complete (or as expensive) as FGC's test
    - Some SNPs are too "flippy" to be of much practical value.

    Leave a comment:


  • DeeTyler
    replied
    Originally posted by lgmayka View Post

    For a very limited time, Full Genomes is also (like YFull) interpreting BAM files at no charge.
    No doubt the help desk is swamped with requests .. but what is the usual wait time after sending an email to the helpdesk to receive a link to DL the BAM file?

    Leave a comment:


  • DeeTyler
    replied
    Originally posted by Rebekah Canada View Post
    Hi,

    I know that Felix has been working on a Y-Merge tool.
    http://www.y-str.org/2014/04/merge-y.html
    I am sure he would appreciate feedback on how it works and what else the community would like to see.
    Thanks! I have results from all three (Big Y, Geno 2, 23 and me), so I'll give it a spin.

    Leave a comment:


  • lgmayka
    replied
    Originally posted by J Honeychuck View Post
    Is there nothing the individual can do with these results? I just want to know how close I am (in generations) to other cases on the ISOGG and FTDNA trees. Is there any way to do that?
    You can do that if you have multiple Big Y results (from the same clade) with which to compare. But even then, you may encounter one major handicap:

    For the Known SNPs, you can distinguish between derived, ancestral, and no-call. But for Novel Variants, you cannot distinguish between ancestral vs. no-call except via the BAM file.

    For a very limited time, Full Genomes is also (like YFull) interpreting BAM files at no charge.

    Leave a comment:

Working...
X