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An error occurred when I tried to convert our sample vcf to GDS format. Even after providing the read, write, and edit permissions for all the input files it is showing the warning. Any thoughts as to where I am going wrong?
Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output # please also include the results of running the following in an R session sessionInfo( )
Set working directory
setwd("D:/R_workspace/WIPRO3/Wipro-3/extdata/") library(vcfR) library(BiocGenerics) library(gdsfmt) library(SNPRelate) library(SeqSQC)
Load the input files
infile <- system.file("extdata", "examples_sub.vcf", package="SeqSQC") sample.annot <- system.file("extdata", "UIMA-F-SE8-2nd-S21.txt", package="SeqSQC") cr <- system.file("extdata", "SureSelectXT_V8_Covered.bed", package="SeqSQC") outdir <- "D:/R_workspace/WIPRO3/Wipro-3" outfile <- file.path(outdir, "testWrapUp") outfile  "D:/R_workspace/WIPRO3/Wipro-3/testWrapUp" seqfile <- sampleQC(vfile = infile, output = outfile, capture.region = cr, sample.annot = sample.annot, format.data = "NGS", format.file = "vcf", QCreport = FALSE) Load vcf file ... Start file conversion from VCF to SNP GDS ... Method: exacting biallelic SNPs Error in VCF_SampID(vcf.fn[i]) : Error VCF format: invalid sample id! In addition: Warning message: In file(filename, "rt") : file("") only supports open = "w+" and open = "w+b": using the former