Question: How To Tell If Bed/Bim/Fam Data Are Phased?
gravatar for Click downvote
6.8 years ago by
Click downvote690 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 6.8 years ago by zx87549.3k • written 6.8 years ago by Click downvote690
gravatar for zx8754
6.8 years ago by
zx87549.3k 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 6.8 years ago by zx87549.3k
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