Creating SNP index

Question

[thulani.m.hewavithana]

Hello, I'm having a problem in creating SNP index of Brassica allopolyploids using gmap. Where can I find the SNP data of Brassica? In order to create a pseudo genome I need to have the SNP index. I have tried the snpindex command of gmap with VCF files created using samtools and freebayes. But it showed errors. Please help!

Thanks in advance.