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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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Gene Centric Coding Annotation fails #41

Closed kwdoyle closed 9 months ago

kwdoyle commented 10 months ago

Hello,

When running the script STAARpipelineSummary_Gene_Centric_Coding_Annotation.r, I am encountering this error:

Error in seqGetData(genofile, paste0(Annotation_dir, Annotation_name_catalog$dir[which(Annotation_name_catalog$name ==  :
  The GDS node "annotation/info/FunctionalAnnotation/rsid" does not exist.
Calls: Gene_Centric_Coding_Info -> info_plof -> seqGetData

The rsids for each variant are not included when annotating the gds files in the earlier steps. Are the rsids supposed to be within the FAVOR database files? I'm using the csv files downloaded from the FAVOR database website and the rsids don't seem to be in there..

xihaoli commented 10 months ago

Hi @kwdoyle,

Thanks for asking. I can confirm that rsID is part of the FAVOR Essential Database. Could you please double check whether your aGDS files based on FAVOR Full Database include rsID as a field? If not, you may exclude rs_num from Annotation_name in STAARpipelineSummary_Gene_Centric_Coding_Annotation.r.

Hope this is clear.

Best, Xihao

xihaoli commented 10 months ago

Hi @kwdoyle, I'd like to check whether this issue has been resolved. If so, please feel free to close it. Thanks!