Xiuwen Zheng

It is the number of the approx. independent Markers.

Please use a single core: **parallel = 1**

`snpgdsSlidingWindow()` does not return the window if it is empty, so the first window starts from 11,888.

Please check and modify your fam file. It says "family ID + individual ID" is not unique.

No multithreaded support.

Could you please try the [SeqArray](http://www.bioconductor.org/packages/SeqArray/) package? `SeqArray::seqVCF2GDS()` could provide you more error information. And try `SeqArray::seqVCF_Header()` which returns the objects of VCF header. You could revise the R object...

You can use the functions in the gdsfmt package to change snp.id in the new GDS file: ``` add.gdsn(f, "snp.id", your_new_snp_id, replace=TRUE) ```

Please use `seqSummary()` in the SeqArray package instead.

`pop_code` is just a vector of characters. Your question is more related to R programming itself, rather than SNPRelate. You can import `pop_code` from a text file: e.g., `pop_code

There are many approaches to estimate relatedness. SNPRelate has no simulation function. `snpgdsPairIBD()` may be useful for you, please see the document of `snpgdsPairIBD()`.