I have vcf files of many individuals that I converted from 23andme raw data. I need to convert vcf files to gds files. I preprocessed the raw data so that all individuals have same rsnpids but when I convert vcf files to gds files many snps are disappearing. All individuals have same common snps which is 677235 snps and converting 1st vcf to gds results with losing some snps. I use snpgdsVCF2GDS(f,gdsfile) for conversion.
For example the output of
Some of 'snp.allele' are not standard (e.g., c/A).
The file name: /home/gulce/Documents/output.gds
The total number of samples: 1
The total number of SNPs: 329020
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 1
The number of biallelic unique SNPs: 223585
After converting all files, none of them has common snps. So, what can I do for not losing the snps during conversion of vcf to gds