EPACTS association analysis

Question

[hellbio]

Hi,

I am completely new using association analysis kind of methods and I recently found EPACTS http://genome.sph.umich.edu/wiki/EPACTS as the most widely used tool for association analysis. We have sequenced 40 samples (cases) and have VCF file with genotypes and frequencies for all the 40 individuals. We would now like to compare the 40 cases with 1000 genomes data to see if there are any SNP:s with a significantly higher frequence among the cases than in the "normal" population. And also to perform gene-burden tests. We have a VCF file from 40 cases and a VCF file from 1000 genomes.

From the manual: Single Variant Test

${EPACTS_DIR}/epacts single \ --vcf ${EPACTS_DIR}/data/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \ --ped ${EPACTS_DIR}/data/1000G_dummy_pheno.ped \ --min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \ --out out/test --run 2

I wonder how to proceed in our scenario, since we have two VCF files i.e.cases and controls in independent files. Could you suggest how to handle this. Any suggestions are valuable.

Answer 1

[das2000sidd]

Merge them using vcf merge in one vcf file. Before merging, sort them, compress them using bgzip and then tabix them to get the index file. After that you should be good to go.