Xiuwen Zheng comments

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                                            Xiuwen Zheng

Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE)

As it said `please consider revising it to 'Number=.'`, please revise the VCF file.

seqParallel with BiocParallel::BatchtoolsParam object ?

Sorry! I have forgot this issue during the pandemic. It is on my radar now. Xiuwen

seqGDS2VCF error after using seqMerge

A quick fix could be: ``` f

seqGDS2VCF error after using seqMerge

In your case, did you merge multiple gds files with different variants? or multiple gds files with different samples?

seqGDS2VCF error after using seqMerge

"seqGDS2VCF is also printing "." filter as NA." It is fixed in the development version: http://www.bioconductor.org/packages/devel/bioc/news/SeqArray/NEWS

Problem in SeqArray::seqVCF2GDS - Parsing the vcf header fails

The line `##INFO=` should be removed. It is not a standard format.

Installation problems

Which version R are you using? Please try updating R to the latest version, or at least R_v4.0

snpgdsLDpruning gives an empty snp dataset

Could you please show me the output of `snpgdsLDpruning()`? The output is something like: ``` SNP pruning based on LD: Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)...

snpgdsLDpruning gives an empty snp dataset

Sorry, I don't know how to fix the problem based on your description. If possible, send me your data file. Best wishes,

Sample.idError with seqVCF2GDS

See: **the total number of variants for import: 3,632** This number is too small, `parallel=6L` does not help at all. I guess `parallel=6L` might trigger a bug when merging the...