How To Convert A Multisample Vcf To A Format That Can Be Loaded In Haploview?

Question

[William]

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?

Answer 1

[Chrispin Chaguza]

You can convert the vcf files to plink (.ped or .map) using vcftools http://vcftools.sourceforge.net/documentation.html#plink

Answer 2

[Scott]

You do not need a .info file (marker information) to load a .ped file into Haploview. The error you are getting is probably from the binary nature of your .ped file. Find a way to convert the binary to a .ped txt file and you will be fine to load into Haploview without a .info file. The info file is only to label the SNPs along the top of the linkage map. You can also make your own file if you want numbers or accessions for your SNPs and their location on a chromosome. I believe the conversion might be possible using PLINK, but I do not have any experience with that software.

The 1000 Genomes converter will only work for a ftp site file from the project, you cannot upload your own VCF file, that's why you need a sample panel file and chromosomal region to extract data from their VCF files.