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Question: haplotype phasing related issues
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gravatar for kas
16 months ago by
kas • 0
kas • 0 wrote:

Dear members, How to code the alleles in a phased file to 0/1?

Selscan is showing :

ERROR:  Alleles must be coded 0/1 only.
beagle plink selscan • 488 views
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modified 16 months ago by ATpoint ♦ 46k • written 16 months ago by kas • 0

Hello, what is the source of your input data?

ADD REPLY • link modified 16 months ago • written 16 months ago by Kevin Blighe ♦ 71k

thank you for your response. I'm using beagle output (.phased files) as input for selscan

ADD REPLY • link written 16 months ago by kas • 0

Selscan accepts hap, VCF, and TPED formats, so, you need to get your Beagle output into one of those. I'm aware that these types of analyses can be nightmares.

ADD REPLY • link written 16 months ago by Kevin Blighe ♦ 71k

How to convert .phased to .hap file?

ADD REPLY • link written 16 months ago by kas • 0

Try to understand both formats and then decide what you need to do.

ADD REPLY • link written 16 months ago by Kevin Blighe ♦ 71k
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