Hi guys Please this is very urgent and I really need help on this.
I have a genotyped dataset in Plink .bim .fam ... file format. This data set that includes may unnamed variants including SNPs and indels. Now I need to create bfiles (.bem .bed and .fam) and .raw data set out of the original data set that has specified the indels like chr1:110299165:I and some of the SNPs it includes apparently are included in my data set but not named with RSID or anything.
Can anyone tell me what I can do to extract all the variants from my data set? before I just used to look for snps by their namebut I do not ever looked for indels before or for a snp that is not named in my data set. I have filterd my dataset befor by using --extract for that I need RSID which I do't have. how plink support this problem? what is the option for that?