Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: haplotype phasing related issues
0
gravatar for kas
4 weeks 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 • 119 views
ADD COMMENT • link •
modified 29 days ago by ATpoint ♦ 25k • written 4 weeks ago by kas • 0

Hello, what is the source of your input data?

ADD REPLY • link modified 4 weeks ago • written 4 weeks ago by Kevin Blighe ♦ 51k

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

ADD REPLY • link written 4 weeks 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 4 weeks ago by Kevin Blighe ♦ 51k

How to convert .phased to .hap file?

ADD REPLY • link written 29 days ago by kas • 0

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

ADD REPLY • link written 29 days ago by Kevin Blighe ♦ 51k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour