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| | | The program is available and described on github: |
| =Download=
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| The program can be downloaded from github: | |
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| https://github.com/e-jorsboe/asaMap | | https://github.com/e-jorsboe/asaMap |
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| <pre>
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| git clone https://github.com/e-jorsboe/asaMap.git;
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| cd asaMap
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| make
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| </pre>
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| So far it has only been tested on Linux systems. Use curl if you are on a MAC.
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| =Example=
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| This an example!!
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| =Input Files=
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| Input files are called genotypes in the binary plink files (*.bed) format [https://www.cog-genomics.org/plink2]. And estimated admixture proportions and population specific allele frequencies. For estimating admixture proportions and population specific allele frequencies [http://software.genetics.ucla.edu/admixture/ ADMIXTURE], can be used, where .Q and .P files respectively can be given directly to asaMap.
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| 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:
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| <pre>
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| -0.712027291121767
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| -0.158413122435864
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| -1.77167888612947
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| -0.800940619551485
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| 0.3016297021294
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| ...
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| </pre>
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| 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.
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| <pre>
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| 0.0127096117618385 -0.0181281029917176 -0.0616739439849275 -0.0304606694443973
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| 0.0109944672768584 -0.0205785925514037 -0.0547523583405743 -0.0208813157640705
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| 0.0128395346453956 -0.0142116856067135 -0.0471689997039534 -0.0266186436009881
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| 0.00816783754598649 -0.0189271733933446 -0.0302259313905976 -0.0222247658768436
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| 0.00695928218989132 -0.0089960963981644 -0.0384886176827146 -0.012649019770168
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| ...
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| </pre>
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| Example of a command of how to run asaMap with covariates included and first running ADMIXTURE:
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| <pre>
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| #run admixture
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| admixture plinkFile.bed 2
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| #run asaMap with admix proportions
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| ./asaMap -p plinkFile -o out -c $COV -y pheno.files -Q plinkFile.2.Q -f plinkFile.2.P
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| </pre>
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| This produces a out.log logfile and a out.res with results for each site (after filtering).
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| =Citation=
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