Announcement of new software

The project's programmer, Vasily Gavrilov (Anode) has released a toolkit for processing genetic data in RAW (23andme) format.

Currently supports (command-line):
1) Half-IBD (Identity by descent) aka HIRs calculations - between 2 or any number of files (in distances and cM);
2) RAW2PED conversion;
3) discovery of regions of homozygosity
4) merging of datasets.

Features under development (C language)
1) PED2RAW conversion
2) conversion between Illumina format of series matrices and PED
3) etc.

http://sourceforge.net/projects/aisconvert/files/

Awaiting STRUCTURE (K=10, N=159) results

The project is awaiting the results of first STRUCTURE run (it is being run as a daemon process on Linux server).Since each STRUCTURE run is computationally intensive job (which is apparently the case when max.numbers of MCMC iterations and minimal periods between "burn-ins" are enabled), the results are expected to arrive after circa 7 CPU days.

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Experiments with relatedness

Yesterday i was investigating metodologies of  pairwise IBD estimation in PLINK software. PLINK allows you to estimate genomewide IBD-sharing coefficients between seemingly unrelated individuals from whole-genome data. In a homogeneous sample, it is possible to calculate genome-wide IBD given IBS information, as long as a large number of SNPs are available (probably 1000 independent SNPs at a bare minimum; ideally 100K or more). The basic PLINK command for IBD calculations is

 

plink --file mydata --genome --min 0.05


which yields information useful for IBD estimation

 

FID1      Family ID for first individual
     IID1      Individual ID for first individual
     FID2      Family ID for second individual
     IID2      Individual ID for second individual
     RT        Relationship type given PED file
     EZ        Expected IBD sharing given PED file
     Z0        P(IBD=0)
     Z1        P(IBD=1)
     Z2        P(IBD=2)
     PI_HAT    P(IBD=2)+0.5*P(IBD=1) ( proportion IBD )
     PHE       Pairwise phenotypic code (1,0,-1 = AA, AU and UU pairs)
     DST       IBS distance (IBS2 + 0.5*IBS1) / ( N SNP pairs )
     PPC       IBS binomial test
     RATIO     Of HETHET : IBS 0 SNPs (expected value is 2)

 

Following the instructions from EMERGE Network article "Visualizing relatedness"  and R graphic libraries (such as ggplot2) one can easily visualize Z1 and Z0, the proportion of markers identical by descent 1 and 0 respectively, for every pair of individuals in the dataset.










Example: Visualizing relatedness of  project's "unrelated" sample of N=159

MDL historical portal

For those of you interested in MDL history, here is a link to the most informative MDL historical portal available at the moment. The portal is supported by Istorinės atminties akademija, Lietuvos Respublikos užsienio reikalų ministerija.

First results: Admixture unsupervised run

I've perfomed an unsupervised Admixture run on all of reference samples, shared by DW.

Leon Kull joins the team

It is my pleasure to announce that Mr.Leon Kull (of HIRsearch) has accepted the responsibilities of  the project's co-admin.