Beagle 4.1 - phasing and IBD using multiple chromosomes

Question

[mstagliamonte]

Hi, BioStars users,

I am trying to use Beagle 4.1 for phasing and IBD analysis on a non-model organism. I am trying to understand how to do it for multiple chromosomes. Should I perform a different iteration for each chromosome, or combine the data in one vcf + one map file?

[Vitis]

I did similar tasks one chromosome at a time based on the assumption that genetic materials on different chromosomes are completely independent with each, i. e. no linkage.