converting vcf into simpler version for downstream analysis

Question

[evafinegan]

Hello,

I have made a multi sample vcf file using freebayes. I want to use it for downstream association analysis. I have calls like:

0/0:37:37,0:37:1499:0:0:0,-11.1381,-135.125 ./.:.:.:.:.:.:.:.

I was wondering whether I can convert these calls into simple format for eQTL analysis using BGData package. I am not sure if that is the way to do this or I need to make a bed file or a SNP matrix for all samples. I want to know some opinions how it can be done. Thank you!

[Nicolas Rosewick]

could you explain which downstream analysis you want to do. Please edit the question to be more specific

[evafinegan]

I have added the information, thank you!