haplotype phasing related issues

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5.1 years ago

kas • 0

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 • 1.6k views

ADD COMMENT • link updated 5.1 years ago by ATpoint 85k • written 5.1 years ago by kas • 0

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Hello, what is the source of your input data?

ADD REPLY • link 5.1 years ago by Kevin Blighe 88k

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

ADD REPLY • link 5.1 years ago by kas • 0

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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 5.1 years ago by Kevin Blighe 88k

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How to convert .phased to .hap file?

ADD REPLY • link 5.1 years ago by kas • 0

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

ADD REPLY • link 5.1 years ago by Kevin Blighe 88k

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