In the case of SNP frequency files for a certain reference population (eg. CEU, YRI, ...) eg.
rs# pos refallele refallele_freq otherallele otherallele_freq
rs10181821 5703 A 0.991 G 0.009
rs10195681 8674 C 0.977 A 0.023
is it that reference haplotypes for the corresponding frequency file will also exist? The reason I am wondering is because we are trying to run and compare several local ancestry inference software (notably LAMP and LAMP-LD), but for 3-way admixture for LAMP it requires frequency files (never requiring reference haplotypes) and LAMP-LD never requires frequency files but always requires reference haplotypes. So since LAMP-LD is decidedly an improvement over LAMP, if reference haplotypes will always be available when frequency files are then we may treat 3-way admixture from LAMP as deprecated and not include it in our analysis (LAMP 2-way does not require any frequency files and may be useful when there are no reference haplotypes available).
Please let me know if anything is not clear. Any help is greatly appreciated, thank you!