I have a problem running EPACTS, while performing Single Variant EMMAX Association Analysis.
I have generated the kinship mateix using snprelate R package and thenrun the simple script below:
#Single Variant EMMAX Association Analysis
echo " performing Single Variant EMMAX Association Analysis"
epacts single --vcf $annvcf --ped $PED --min-maf 0.001 --kin $kin --pheno DISEASE --cov SEX --test q.emmax --out $out_dir/annvcf.q.emmax --run 24
what I get in the output is:
FATAL ERROR - MAGIC number for kinship matrix does not match
I have refined the pedigree and made the kinship matrix again, but the error is the same.
I am very new to this software, it will be very nice if you have any tips which can help me solving this issue.