I am trying to make LD plot using Haploview from 1000 genomes project data for a list of SNPs. As usual there are problems with input files, I was trying the VCF to PED converter from 1000 genomes websites to make .ped and .info files but when trying to load on Haploview (under PLINK format) an error raised: Improper map file formatting on line 1.
I wonder if anyone can help me to circumvent this error.
Any comments would be highly appreciated.
Thank you All.
Regards