Announcement

Collapse
No announcement yet.

Well, so much for that...

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

  • #31
    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.

    Comment


    • #32
      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-)

      Comment


      • #33
        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.

        Comment


        • #34
          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?

          Comment


          • #35
            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

            Comment


            • #36
              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).

              Comment


              • #37
                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..

                Comment

                Working...
                X