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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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Importing DArT file and converting to VCF #54

Closed pezhmansafdari closed 4 years ago

pezhmansafdari commented 5 years ago

Hi, I am trying to import a DArt file and convert it to VCF because I want to calculate nucleotide diversity. When I use the command:

SNP <- radiator::read_dart("Report_DPlan16-2487_SNP_singlerow.csv", strata="dart.strata.tsv")

I get the following error:

Reading DArT file... Number of blacklisted samples: 0 DArT SNP format: genotypes in 1 Row Generating genotypes and calibrating REF/ALT alleles... Number of markers recalibrated based on counts of allele: 8759 Generating GDS... Error in SeqArray::seqVCF2GDS(vcf.fn = paste0(temp.file, ".vcf"), out.fn = if (length(filename) > : There is no sample in the VCF file.

Would you please tell me what could be the source of the problem?

All the bests, Pezhman Safdari

zhengxw-ab commented 5 years ago

You might need to update your installed SeqArray package, and the latest SeqArray can import a VCF file with no sample.