convert vcf to hapmap

[sandesh]

I was trying to use SNPhylo software.
I needed to combine multiple SNP vcf files together or use combined hapmap file.
Is there any way to get single vcf or hapmap file with multiple samples together?

[GenoMax]

bcftools-merge? http://vcftools.sourceforge.net/htslib.html#merge

[sandesh]

bcftools-merge? http://vcftools.sourceforge.net/htslib.html#merge

Thanks I tried vcf-merge

[lalchung]

@sandesh
i am trying to run SNPhylo.do i need all the VCF, Simple SNP file and hapmap file ??or i need just one of these files.pls help

[yzzhang]

I fed SNPhylo only a VCF file and it ran smoothly. If you use SNPhylo, please check the sam headers, it seems SNPhylo only accept number as chromosome header (e.g. >1 but not >chr1) at least for old SNPhylo version (2014.....). Hope it helps.

[lalchung]

SNPhylo

hi yzzhang, i appreciate your help. I have this project to find SNPs across 5 different population and build a phylogenetic tree. so, for my VCF file should i combine all the SNPs from all population into one VCf file and then run SNPhylo??