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Thread: EDIT / may be incorrect assumption

  1. #1
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    EDIT / may be incorrect assumption

    [[[ EDIT: I may be misreading the .VCF files. so I may have to strike this. Holding. ]]]
    Last edited by Mikewww; 03-28-2014 at 08:59 PM. Reason: May have some incorrect info so waiting for confirmation.

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  3. #2
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    dubh$ cut -f1 -d' ' mikes-list.txt
    13494176
    14480546
    21477811
    23311208
    14478992
    14479010
    dubh$ for i in `cut -f1 -d' ' mikes-list.txt `
    > do
    > grep $i ~/new/xxxxxxx/variants.vcf
    > done
    chrY 13494176 . A G 20.4486 REJECTED . GT 1
    chrY 14480546 . C . 1484.13 PASS . GT 0
    chrY 21477811 . A AAAAGAAAG 1484.13 PASS . GT 0/1
    chrY 23311208 . C . 1484.13 PASS . GT 0
    chrY 14478992 . G T 1484.13 PASS . GT 0/1
    chrY 14479010 . C T 1484.13 PASS . GT 0/1

    Most of these show up in a R1a individual so they are upstream of R1b.

    -Paul
    (DF41+)

  4. #3
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    Quote Originally Posted by Dubhthach View Post
    dubh$ cut -f1 -d' ' mikes-list.txt
    13494176
    14480546
    21477811
    23311208
    14478992
    14479010
    dubh$ for i in `cut -f1 -d' ' mikes-list.txt `
    > do
    > grep $i ~/new/xxxxxxx/variants.vcf
    > done
    chrY 13494176 . A G 20.4486 REJECTED . GT 1
    chrY 14480546 . C . 1484.13 PASS . GT 0
    chrY 21477811 . A AAAAGAAAG 1484.13 PASS . GT 0/1
    chrY 23311208 . C . 1484.13 PASS . GT 0
    chrY 14478992 . G T 1484.13 PASS . GT 0/1
    chrY 14479010 . C T 1484.13 PASS . GT 0/1

    Most of these show up in a R1a individual so they are upstream of R1b.

    -Paul
    (DF41+)
    I apologize if I'm misreading the .vcf files for U152. I was using this process to remove upstream from L21.

    What's the "." stand for in the derived column? Is that just a "no call"? If so, I'm all wet on the presumption.

    Maybe I should pay more attention to the right most column. I clearly need a lesson in .vcf files.

    How do you interpret these?
    chrY 14480546 . C . 16.1001 PASS . GT 0
    chrY 23311208 . C . 1484.13 PASS . GT 0

    There is "." in the ALT column. Does that just mean "no call" and therefore you have to go to the .BAM files?

    This group that I was eliminating as upstream of L21 (about 200 variants) so they were derived, but the wave 1 variant files were handled differently so there could be more to it, as well.
    Last edited by Mikewww; 03-28-2014 at 09:25 PM.

  5. #4
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    Here is the 1000 Genome link might give some insite but some information is not provided by FtDNA but they can be asked.

    http://www.1000genomes.org/wiki/Anal...mat-version-41

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1’s father’s sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  6. #5
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    Mike, don't be to quick to bin this there could be some legs to it.

    I'm finding

    13494176G
    21477811AAAAG
    23311208T
    14478992T
    14479010T

    in Z18 kits but not

    14480546T

    These others could easily be variations in HUGO with L21 having the ancestral value. Much of HUGO is U152, right ?

    How many P312 xL21 & DF19 kits have you access to ?

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