Input file of Haploview

Question

[Đạt]

Hello everyone, I am using Haploview to find the tag SNPs in my data. while preparing the input file, the format ask for .info file which include the SNP id and the position. No Chromosome information is asked to input. So how can Haploview know whether the variant is in right position or not. We can use the ped file directly from the plink file, can't we? Many thanks

Answer 1

[LauferVA]

Because the algorithm does not rely on knowing the identity of a chromsome, contig, etc.; it requires only the degree of linkage between the variants and their order.

Haploview was designed of course for cases in which that info may in fact be known - but also for cases in which it is not. Even when it is known, that information adds nothing to the plot itself other than, potentially a title or some such.