SeqArray
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zhengxwen
Data management of large-scale whole-genome sequence variant calls (Development version only)
Dear Sir Now I am learning to use SeqArray package. I am trying to use the package to convert my Exome VCF SNP file into SNPGDS file for SNPrelate package...
I have a VCF file that consists of structural variant records. I'm trying to convert vcf to gds, but failed. The command I used is: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option="ZIP_RA", parallel=8L) The...
Hi, I get an error when I'm trying to convert from a vcf file to a gds file using the SeqArray package. Here is my code and the error message....
Erreur dans AsDataFrame(s[i], c(T = "ID", T = "Number", T = "Type", T = "Description", : No 'ID'. Parsing the VCF header fails. I don't know why I have this...
Hi I am trying to install SeqArray but I have been having the same issue. I restarted all but it is still hapening. Could somebody help me please. if (!requireNamespace("BiocManager",...
Hi @zhengxw-ab I am interested to create GDS file using VCF from imputed data. I would like to keep dosage information intact in this process. I use command as: `...
Hi, I'm trying to run snpgdsIBDMLE function from the SNPRelate package on a seqArray obtained from your example : file
Came across an issue where using seqGDS2SNP() on a "SeqVarGDSClass" object housing haploid variant calls that had been filtered. Effectively the process alters the genotypes, with the resulting "SNPGDSFileClass" object's...
After having merged some gds files I am getting an error with seqGDS2VCF due to seqSummary() This stems from the .summary_filter() function were the attributes of the merged gds seems...
Hi, amazing resource of tools built here! I have a question regarding the seqParallel function. I can see the `cl` arguement takes a BiocParallelParam object. I attempted to use it...
