Changes

</pre>  

</pre>  

<br> Run the single variant score test on the example data using this command:  

<br> Run the single variant score test on the example data using this command:  

<pre>${EPACTS_DIR}/epacts single  

<pre>${EPACTS_DIR}/epacts single \

--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz  

--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \

--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped  

--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped \

--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno  

--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \

--out {OUTPUT_DIR}/test --run 2 &amp;

--out {OUTPUT_DIR}/test --run 2 &amp;

</pre>  

</pre>  

This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001. &nbsp;The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. &nbsp;The output file directory prefix is {OUTPUT_DIR}/test. &nbsp;Finally, EPACTS will run the analysis in parallel on 2 CPUs.

This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001. &nbsp;The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. &nbsp;The output file directory prefix is {OUTPUT_DIR}/test. &nbsp;Finally, EPACTS will run the analysis in parallel on 2 CPUs.