Illumina did my WES and returned very complex and bizzare sample.id like "SampleCU-18" and "Sample24" despite I supplied them with simple 3 digit code 018, 024. When I ran SeqVarData: seqData <- SeqVarData(gds, sampleData=annot) it returned the following error:

Error in SeqVarData(gds, sampleData = annot) : sample.id in sampleData does not match GDS file

I did make sure the sample.id in annot match exactly.

Does it need to be sorted? How do I sort a gds file based on sample.id? Can I rename the sample.id to something simple like 018 and 024 to avoid error?

Please tag posts with the package name (not the name of an object within the package); otherwise there is no guarantee the maintainer will see them.

My best guess as to what is going on here is that you made your sample.id a factor instead of a character.

https://support.bioconductor.org/p/123007/