STR data from the 1K Project

Moderators: Rootsy, GregRM


Posts: 70
Joined: Wed Mar 14, 2012 7:43 pm
Location: Maine
YDNA:
R1b-M157.2 (under Z6
MtDNA:
J1c2g
PostPosted: Sat Nov 03, 2012 6:30 pm
palamede wrote: ...

I don't understand what is the subject really.
The commercial companies give STR results of a lot of STRs in Y-chr with a very big accuracy and seem not to get any problem of mapping the STR reads to know the number of repeats for a known STR.
...


One of the reasons why I created this thread is to see if was possible to find out some of the STR values for the individuals in the 1K Genome Project. These individuals have not been tested at FTDNA (or at least we cannot match any FTDNA result to any 1K Genome kit). If we were able to tease out the STR results for the 1K Genome, we may be able to make better SNP predictions for folks. In addition, we may be able to tell if some SNPs (such as Z80-Z84 below Z326) are possibly private/family SNPs (and by coincidence two "cousins" were tested in the 1K Genome project) or whether they are more diverse, but restricted in a regional way (as Z80-Z84 were all discovered in two samples from Colombia, but have not yet been found despite fairly widespread testing at FTDNA).
Y Haplogroup: R1b - U106 - L48 - Z8 - Z6 - M157.2 (private sub-clade of Z6). 111 markers tested, Palindromic markers tested
mt Haplogroup J1c2g Full Mitochondrial test with an additional (private) mutation at 9974T
YSearch & Mitosearch ID: 3HSPN
User avatar
Posts: 182
Joined: Wed Mar 14, 2012 12:30 pm

YDNA:
Z1297*
MtDNA:
J1c5a*
PostPosted: Sat Nov 03, 2012 6:58 pm
Alignment problems exist especially we have short reads and short tandem repeats the program is difficult to make good alignment. Each of 1000 Genomes sample have sequencing of different quality (35-100 bp) and alignment because good segments can not match. I said that in some samples from 100 loci we can extracted within 40-70 loci.And all of these can be different within this one hundred. :)
M102+ Project

---
Grandpa: R1a-L366
User avatar
Posts: 287
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Wed Feb 27, 2013 7:27 pm
Y-STRs from Y-sequence data: I'd like to discuss about lobSTR, a software script, which was used to extract Y-STR from 1000 Genome data.
The paper was quite discussed arround 17 Feb.: Identifying Personal Genomes by Surname Inference
The software: lobSTR: A short tandem repeat profiler for personal genomes
See also: lobSTR algorithm rolls DNA fingerprinting into 21st Century

I have tried to extract STR-Marker values from a 1000 Genome sample (NA21090) using lobSTR script. I was not able to setup the script to extract only the interesting Y-STRs (had to interrupt full genome extraction after hours of calculation). After I tried to extract them manually using Supplemental Material Table S5, but I did too much errors and it was no good workflow. If anyone has advise I would appreciate.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
User avatar
Posts: 182
Joined: Wed Mar 14, 2012 12:30 pm

YDNA:
Z1297*
MtDNA:
J1c5a*
PostPosted: Wed Feb 27, 2013 7:31 pm
Our program is much better.
M102+ Project

---
Grandpa: R1a-L366
Previous

Return to 1K Genomes Project

Who is online

Users browsing this forum: No registered users and 1 guest