Question: ADMIXTURE results - how can I determine what SNPs are associated with different inferred ancestry components?
3
gravatar for devenvyas
3.8 years ago by
devenvyas570
Stony Brook
devenvyas570 wrote:

I have some ADMIXTURE results that I am struggling to plot, but I am interested in determining what SNPs are going into which components. I know that ADMIXTURE itself does not specify which components correspond to which SNPs. I was wondering if anyone has any suggestions on how I could do this.

I am looking into ELAI, LAMP, and HAPMIX, but I am open to suggestions.

Thanks!

snp admixture • 2.7k views
ADD COMMENTlink modified 3.8 years ago by Gabriel R.2.6k • written 3.8 years ago by devenvyas570
0
gravatar for Gabriel R.
3.8 years ago by
Gabriel R.2.6k
Center for Geogenetik Københavns Universitet
Gabriel R.2.6k wrote:

You don't really have SNPs associated with a particular ancestral component but rather, an estimate of allele frequency in each ancestral component. That's the P file. See the manual page 3:

https://www.genetics.ucla.edu/software/admixture/admixture-manual.pdf

ADD COMMENTlink written 3.8 years ago by Gabriel R.2.6k

I already know that, I want to know if there is an alternate program I can use to cut portions of the genome into different ancestries.

ADD REPLYlink written 3.8 years ago by devenvyas570
1

Ah then have a look at ChromoPainter and fineStructure 

http://www.paintmychromosomes.com/

ADD REPLYlink written 3.8 years ago by Gabriel R.2.6k

in that case, many of the programs you listed are a really good place to start, essentially you are asking about local ancestry estimation, for which ELAI, LAMP, HAPMIX, chromosome painter etc. are good alternatives.

There also programs that use local ancestry to increase power for association testing if that is of interest to you, in this case maybe start by reading http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002325 

the same author wrote a fairly good review in 2013 .. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556814/ 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Vincent Laufer1.0k

I'll look into chromopainter as well then. I am not really interested in association testing. I am just looking for Neanderthal in different parts of the genome.

ADD REPLYlink written 3.8 years ago by devenvyas570

I remember Sriram Sankararaman did something along those lines for the Altai Neanderthal paper. Have a look at this maybe:

http://www.nature.com/nature/journal/v505/n7481/full/nature12886.html#/denisovan-gene-flow-in-mainland-asia

He essentially used an HMM to identify these chunks in phased genomes.

ADD REPLYlink written 3.8 years ago by Gabriel R.2.6k
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