Question: haplotype phasing related issues
0
gravatar for kas
4 weeks ago by
kas0
kas0 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 • 119 views
ADD COMMENTlink modified 29 days ago by ATpoint25k • written 4 weeks ago by kas0

Hello, what is the source of your input data?

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Kevin Blighe51k

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

ADD REPLYlink written 4 weeks ago by kas0

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 REPLYlink written 4 weeks ago by Kevin Blighe51k

How to convert .phased to .hap file?

ADD REPLYlink written 29 days ago by kas0

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

ADD REPLYlink written 29 days ago by Kevin Blighe51k
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