Eagle2 Phasing VCF files

Question

[pmbock1]

I am working on phasing vcf files using EagleImp-Web, a web tool that uses Eagle2 and a reference panel (1000 genomes or HRC) to phase variants per chromosome. For my research, I only need about 100 variants split among 10 chromosomes to be phased. Does phasing effectiveness rely on the number of variants included within a vcf file? I could provide a vcf with all variants within each chromosome, then filter out the ones I need. Or a vcf with just the variants I need for my research, which is much faster. I am confused about how reference panel Eagle2 phasing works.

Answer 1

[4galaxy77]

Yes, phasing definitely relies on the number of SNPs present in the input VCF. Specifically, it relies on having multiple SNPs which are in LD which are in LD with one another. So as a general rule, include as many SNPs as you can and then subset afterwards. Only including 100 SNPs across 10 chromosomes would give you garbage results.