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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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Lack of Input Examples for running STAARpipeline #30

Closed cantlap closed 1 year ago

cantlap commented 1 year ago

Thank you for designing such a useful tool with STAARpipeline.

I am stuck on the summary portion of the pipeline due to the not knowing what the known loci info csv should look like or contain. This is the line in the the R script file: "STAARpipelineSummary_Known_Loci_Pruning.r" within step 0 of the summary step: known_loci_info <- read.csv("/path_to_the_file/TOPMed_F5_LDL_Known_Loci_info.csv"). I was hoping to see what the csv format should look like, what information/columns it should contain and how to format it. In addition, is there any way to include some example input files for reference along the way in the other steps too (such as an example phenotype file or any other csv inputs).

The example R scripts and Shell scripts are very helpful in knowing how to run the pipeline but I have found myself stuck on steps with additional required inputs.

Thank You!

xihaoli commented 1 year ago

Hi @cantlap,

Thank you for your suggestions. We will do our best to include some examples in the STAARpipeline-Tutorial.

For your specific question on the known_loci file, feel free to send an email and I am happy to explain more.

Best, Xihao