Question: converting vcf into simpler version for downstream analysis
0
gravatar for evafinegan
26 days ago by
evafinegan0
evafinegan0 wrote:

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!

snp • 102 views
ADD COMMENTlink modified 26 days ago • written 26 days ago by evafinegan0

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

ADD REPLYlink written 26 days ago by Nicolas Rosewick9.2k

I have added the information, thank you!

ADD REPLYlink written 26 days ago by evafinegan0
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