216
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
</pre>
</pre>
Run the single variant score test on the example data using this command:
Run the single variant score test on the example data using this command:
<pre>${EPACTS_DIR}/epacts single --vcf ${EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --ped ${EPACTS_DIR}/example/1000G_dummy_pheno.ped --min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno --out /net/nfsb/snowwhite/home/maclemen/test.epacts --run 2 &
<pre>${EPACTS_DIR}/epacts single \
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped \
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
--out {OUTPUT_DIR}/test --run 2 &
</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. The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. The output file directory prefix is {OUTPUT_DIR}/test. Finally, EPACTS will run the analysis in parallel on 2 CPUs.
== 2. Convert the minimac or Impute2 output into VCF format ==
== 2. Convert the minimac or Impute2 output into VCF format ==
