Xiuwen Zheng

GWASTools (

`snpgdsGDS2PED()` and `snpgdsGDS2BED()` do not have such function. But I could consider adding the function in future.

You will need the [SeqArray](http://www.bioconductor.org/packages/SeqArray) package to import the VCF file, Here is the example for using `snpgdsLDpruning()` and `seqExport()` to export to a GDS file: http://www.bioconductor.org/packages/release/bioc/vignettes/SAIGEgds/inst/doc/SAIGEgds.html#preparing-snp-data-for-genetic-relationship-matrix

You should just use SeqArray GDS. The GDS file defined in SeqArray is an extension of SNPRelate GDS. `snpgdsLDpruning()` can work on SeqArray GDS. Best wishes, Xiuwen

See: http://www.bioconductor.org/packages/release/bioc/vignettes/SeqArray/inst/doc/SeqArray.html#integration-with-snprelate

SeqArray GDS is the second generation of SNPRelate GDS. Please use `snpgdsLDpruning(..., autosome.only=FALSE)`, since the chromosome coding in your file is not numeric (not identified as autosomes).

It might be "no sufficient memory".

Show me `sessionInfo()`

Please try the latest version SNPRelate_v1.12.1 on github: ``` library("devtools") install_github("zhengxwen/SNPRelate") ``` This version fixes 'LENGTH or similar applied to NULL object' in the C codes, and it might be...

I have been searching the information about `_ZNSs6assignERKSs`. It seems that you are likely mixing and matching gcc version. I don't have much suggestion, but please try reinstalling gdsfmt and...