Following is the pipeline for carrier frequency which I tried, kindly look into it and let me know: Using merged vcf, Command 1) vcftools --vcf filenameofmergedvcf.vcf --out filename --plink This will create .ped and .map files
Command 2) plink --file filename --freq This will create the .hwe file which is the file containing the carrier frequencies.
BUT if the frequency of the alternate allele is greater than 0.05. It represent ref allele as alternative.
can someone help me why this is happening and how i can resolve this issue?