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Mikewww
03-28-2014, 06:57 PM
[[[ EDIT: I may be misreading the .VCF files. so I may have to strike this. Holding. ]]]

Dubhthach
03-28-2014, 07:25 PM
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+)

Mikewww
03-28-2014, 08:49 PM
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.

MJost
03-28-2014, 09:20 PM
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/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

MJost

jdean
03-28-2014, 11:12 PM
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 ?