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I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, GATK, and vcftools).

Obviously they all probably have their uses and you could likely spend a while discussing this, but can anyone give a short, simple explanation as to whether the methods are generally the same, or whether one or another is generally best for certain situations? Thanks!

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2 Answers 2

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Given that Plink reads in VCF files natively, and Plink is your desired output format, I expect that plink --vcf <file> would be the best option.

As mentioned by @sarah, Plink uses the sample IDs to create family/individual IDs, see "Variant Call Format" section on this page:

VCF files just contain sample IDs, instead of the distinct family and within-family IDs tracked by PLINK. We offer three ways to convert these IDs:

--double-id causes both family and within-family IDs to be set to the sample ID.
--const-fid converts sample IDs to within-family IDs while setting all family IDs to a single value (default '0').
--id-delim causes sample IDs to be parsed as <FID><delimiter><IID>; the default delimiter is '_'. If any sample ID

does not contain exactly one instance of the delimiter, an error is normally reported; however, if you have simultaneously specified --double-id or --const-fid, PLINK will fall back on that approach to handle zero-delimiter IDs.

If none of these three flags is present, the loader defaults to --double-id + --id-delim.

There are caveats associated with the types of variants that Plink will pull in from the VCF files, mostly related to limitations of Plink's own file formats. But if your end-goal is Plink, then that should be fine.

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Additional tidbit I learned in the last year that I wanted to share with anyone else that's working on this.

Plink creates an extremely generic fam file for you, but if you are updating this fam file to reflect your population's family structure, sex, etc., note that when using plink binary files (bed/bim/fam) the order of the individuals in the fam file needs to match the order of the individuals in the other files (which is the order of the individuals in the generic fam file)

Do be careful if you care about which alleles are major/minor, as sometimes the order gets switched around in plink. For more info see "Variant Call Format" section on this page.

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