Question: haplotype phasing related issues
0
gravatar for kas
16 months 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 • 488 views
ADD COMMENTlink modified 16 months ago by ATpoint46k • written 16 months ago by kas0

Hello, what is the source of your input data?

ADD REPLYlink modified 16 months ago • written 16 months ago by Kevin Blighe71k

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

ADD REPLYlink written 16 months 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 16 months ago by Kevin Blighe71k

How to convert .phased to .hap file?

ADD REPLYlink written 16 months ago by kas0

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

ADD REPLYlink written 16 months ago by Kevin Blighe71k
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