I have generated a plink file from a vcf file using vcftools. This is the command I used:
tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr13.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 13:19000000-19050000 |vcftools --vcf - --indv HG00096 --plink
vcftools generate 2 files (out.ped and out.map) and I want to load them into Haploview.
According to Haploview's documentation, Haploview accepts now plink generated files. And these are the requirements according to the User's guide:
"Output files from PLINK can be loaded into Haploview using the PLINK tab on the initial loading screen. PLINK files must contain a header and at least one column header must be titled "SNP" and contain the marker IDs for the results in the file. PLINK loading also requires a standard PLINK map or binary map file corresponding to the markers in the output file. The map file can be either three or four headerless columns (the Morgan distance column is optional)"
I have tried with out.ped and out.map that were generated by vcftools and they do not work in Haploview, and reading the documentation it is not quite clear to me how the .ped file has to be formatted in order to be accepted by Haploview
Could anyone help me with this?