Question: How To Tell If Bed/Bim/Fam Data Are Phased?
gravatar for Click downvote
5.9 years ago by
Click downvote670 wrote:

For VCF files the rule is "pipe means phased, slash unphased". See A: Phased and unphased genotypes in VCF files: does the order of alleles matter?

Is there such a rule for the bed/bim/fam family of files?

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ADD COMMENTlink modified 5.9 years ago by zx87548.0k • written 5.9 years ago by Click downvote670
gravatar for zx8754
5.9 years ago by
zx87548.0k wrote:

As far as I know, bed/bim/fam is a plink binary format of regular ped/map format, which is not a phased format.

See SHAPEIT for examples of file formats.

ADD COMMENTlink written 5.9 years ago by zx87548.0k
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