Extract certain SNPs and indeld from a genotyped dataset.
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4.3 years ago
Mazza ▴ 40

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?

SNP indel rsid .raw data .bim file • 1.3k views
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