Xiuwen Zheng

Yes, if Plasmodium falciparum genomes are in the diploid state.

Try `snpgdsVCF2GDS()` in the SNPRelate.

I am afraid I do not agree that Allele1 should always

The function `snpgdsCombineGeno` compares `snp.allele` to determine whether the alleles are inverted. However, sometimes some alleles are from the reverse strand not the forward strand, which could cause an issue...

I think you have missed something: I have checked the source code carefully. I change coding from PLINK BED to GDS correctly at SNPRelate.cpp (line 877 to 911): ``` const...

We use 2 bits to store a SNP genotype, which is defined as the count of the reference allele. So "(0|0)" should be coded as 2, since "0" represents reference...

Cannot recognize `None` in `COVERAGE=None,0,8,8,8`. `None` should be replaced by `.` in the VCF file!

> Currently SeqVarTools determines ploidy of a GDS file using the first dimension of the genotype node: https://github.com/smgogarten/SeqVarTools/blob/devel/R/AllUtilities.R#L20 > > Is there an alternate way to get the ploidy if...

Could you please show me the structure of your gds file? like, ```R f

See: ``` | |--+ data { Bit2 1x51x132 LZMA_ra(49.1%), 833B } * ``` It is expected to be `Bit2 1x51x49763` (or at least 49763). Here `1` is the ploidy, `51`...