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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
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Generate GDS files #9

Closed daniel-hui closed 1 year ago

daniel-hui commented 1 year ago

Hi Xihao,

We are trying to run STAARpipeline for rare non-coding variants. I had a question for "Step 1: Generate the variants list to be annotated". Is the user meant to generate GDS files on their input data using SeqArray (before using Varinfo_gds.R), or are these files already provided? If so, do you have example code on how to do generate them? Is something like the example here on pages 3-5 intended? I am not familiar with GDS files or the SeqArray package and I wanted to check first. Thanks.

Daniel

xihaoli commented 1 year ago

Hi Daniel,

Thanks for your question. Your understanding is correct; the user meant to generate GDS files on their input data using SeqArray (before using Varinfo_gds.R). We have provided example scripts to convert VCF/BCF files to GDS files using the seqVCF2GDS or seqBCF2GDS functions in the SeqArray package. You may also use the seqBED2GDS or seqSNP2GDS functions to convert other file formats to the GDS format.

Best, Xihao