Effective genome size for MACS2 in allele specific Chip-Seq

Question

[liang795]

Hello,

I am using MACS2 to call peaks for allele specific Chip-seq result. However, I am not sure how I should set the effective genome size for it. Since I used SNPs to distinct different allele-mapping, the effective genome size for G1 and G2 should be different, but should I use the effective genome size estimated from the whole genome or I should use a different genome size for different alleles? If so, may I know how I should calculate that? Thank you so much!