I'm using GWASTools for my GWAS analysis. It turned out that there are some genotyping problems with a few hundred SNPs on the X-chromosome. I already have all my data stored in gds files for use in GWASTools and I want to change the genotypes of the erroneous SNPs directly in the gds file. I was hoping there is kind of a "setGenotype" function with works exactly like the "getGenotype" function that I use to obtain specific SNP genotypes, but couldn't find anything like that.
Did I miss anything? How can genotype changes of specific SNPs be done in gds files without going back to raw data file and creating a new gds file based on them?
Thank you for your help!