Question: Merging a PLINK file with itself after duplicating sampleIDs and rsIDs
gravatar for aritra90
22 months ago by
United States
aritra9040 wrote:


I want to merge a PLINK file with itself, maintaining high genotyping rate. Let's say I have a file test.bed/bim/fam, what I am doing is the following:

  1. randomly selecting few SNPs from test.bim into a file snpstoflip.txt
  2. flipping those SNPs using

    ./plink --bfile test --flip snpstoflip.txt --make-bed --out flipped_test

  3. Duplicating the samples and SNP ids for the flipped_test dataset. (Adding something like "Dup_" infront of each sampleIDs and rsIDs)

  4. Merge them using

    ./plink --bfile test --bmerge flipped_test --make-bed --out MergedFiles

But, doing this, the genotyping rate decreases a lot, to 0.5, that means we have a lot of missing entries. Is there a better way of achieving this? The idea is to replicate the PED file many times to generate a scaled up large data set from a relatively small data set. Please let me know, your views on this or how to tackle this problem, without getting a lot of missing entries.


genotype snp plink merging • 727 views
ADD COMMENTlink written 22 months ago by aritra9040
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1337 users visited in the last hour