Marker trait associations using LASSO regd.

Hi,
I have a SNP genotype file (in VCF format) and a trait file and I want to study the marker trait association using LASSO. Is there any tool for same? I found one tool viz. LPS (Lasso patternsearch algorithm). This tool accepts a tabular input. If this tool will perform the association, I am not sure because I tried to convert the vcf to tabular format through multiple steps and finally got nothing.
Crop galaxy site has a LASSO tool which requires the input file in binary format. I converted the vcf file to binar format (bed) using plink and used same as input file in crop galaxy. Still I am not getting the results.

Hi @susheel_raina

The format of the input is described on the tool form down in the Help section. The data format is the same as would be input outside of Galaxy. That means that manipulations described generally on the web or in publications would apply. Most of not all of that can be done in Galaxy.

Do you want to troubleshoot this part? We’ll need more data details to help.

From what I can tell, the tool is the same between the http://cropgalaxy.excellenceinbreeding.org/ and UseGalaxy.eu server. The input is a tabular file with “binary” columns of data – meaning, an encoded set of numbers but still plain text with a tabular datatype.

I asked a member of our team that specializes in Machine Learning, and these were his comments:

If they want to perform regression analysis, we do offer Ridge (and not Lasso) regression under “Generalized linear models” – It’s a similar tool.

Tutorials for that usage can be found at → Statistics and machine learning / Tutorial List

Let’s start there. :slight_smile: