AsaMap

Download

The program can be downloaded from github:

https://github.com/e-jorsboe/asaMap

git clone https://github.com/e-jorsboe/asaMap.git;
cd asaMap 
make

So far it has only been tested on Linux systems. Use curl if you are on a MAC.

Example

This an example!!

Input Files

Input files are called genotypes in the binary plink files (*.bed) format [1]. And estimated admixture proportions and population specific allele frequencies. For estimating admixture proportions and population specific allele frequencies ADMIXTURE, can be used, where .Q and .P files respectively can be given directly to asaMap.

A phenotype also has to be provided, this should just be text file with one line for each individual in the .fam file, sorted in the same way:

-0.712027291121767
-0.158413122435864
-1.77167888612947
-0.800940619551485
0.3016297021294
...

A covarite file can also be provided, where each column is a covariate and each row is an individual - should NOT have columns of 1s for intercept (intercept will be included automatically). This file has to have same number of rows as phenotype file and .fam file.

0.0127096117618385 -0.0181281029917176 -0.0616739439849275 -0.0304606694443973
0.0109944672768584 -0.0205785925514037 -0.0547523583405743 -0.0208813157640705
0.0128395346453956 -0.0142116856067135 -0.0471689997039534 -0.0266186436009881
0.00816783754598649 -0.0189271733933446 -0.0302259313905976 -0.0222247658768436
0.00695928218989132 -0.0089960963981644 -0.0384886176827146 -0.012649019770168
...

Example of a command of how to run asaMap with covariates included and first running ADMIXTURE:

#run admixture
admixture plinkFile.bed 2

#run asaMap with admix proportions
./asaMap -p plinkFile  -o out -c $COV -y pheno.files -Q plinkFile.2.Q -f plinkFile.2.P

This produces a out.log logfile and a out.res with results for each site (after filtering).