Question: Plink allele with frequency greater than 0.05
0
gravatar for dishasharma35
28 days ago by
dishasharma350 wrote:

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?

ADD COMMENTlink modified 27 days ago by genomax75k • written 28 days ago by dishasharma350
0
gravatar for chrchang523
28 days ago by
chrchang5236.1k
United States
chrchang5236.1k wrote:

Use plink 2.0 —vcf to directly import the VCF when you need to keep track of REF/ALT alleles.

ADD COMMENTlink written 28 days ago by chrchang5236.1k
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