Closed dylanHco closed 1 year ago
It is difficult to solve the problem based on the information here.
But you could try SNPRelate::snpgdsVCF2GDS()
to convert VCF to GDS.
Thanks Xiuwen, I think that did the trick! It seems to be working now, I will close the the issue and reopen if I run into any other issues!
I was using this to import the VCF:
SeqArray::seqVCF2GDS(vcf.fn = filename, out.fn = filename.gds, optimize = TRUE, scenario = "imputation",ignore.chr.prefix = "chr")
Hello -
I am trying to generate a PCA after already importing my vcf file and converting it to GDS file format.
pca.out = SNPRelate::snpgdsPCA(autosome.only = F, gdsin) After running this i get the following error:
Error in .DynamicForkCall(njobs, njobs, .fun = function(.jobidx, ...) { : Error in seqApply(f, nm, as.is = "none", FUN = .cfunction(cn), .useraw = NA, : Invalid position in CIndex.
My vcf file was generated with STACKS.
Any thoughts? Thanks!