How can I convert a multisample vcf file to a format that can be loaded in Haploview?
I have WGS SNP calls for a set of 10 inbred animals and I want to explore haplotype blocks in Haploview.
On the GATK website I already found GATK VariantsToBinaryPed, it can output a binary ped, bim(?) and fam(?) file. I am not sure if haploview can read the binary ped file, the haploview tutorial has a text ped file. According to the tutorial I also need a marker information ( .info) file. Loading the binary ped file without the info file results a failure that the file can't be loaded (with no more info).
I also found the 1000 genomes vcf to ped converter which can convert a vcf to a ped file and marker information file. But this one requires me to supply a sample_panel_file(?) and a chromosomal region?
Are there other converters that I can use? Why does haploview need a marker information file? Can I do a haplotype analysis in haploview with my set of millions of SNPs in 10 inbred animals or do I need a lower set of SNPs / higher set individuals?