I have genotypes data for 2 population, both in binary format (.bed, .bim, .fam). 1st population, consist of 1 parent and 107 progenies. 2nd population only consist of 50 progenies only.
Since the 2nd population didn't have genotype data for parent, I would like to extract parent's SNPs data from the 1st population since there are closely related, and then merge it into 2nd population.
Plink provide function
--bmerge. To retrieve parent data, I used:
plink --bfile file --keep parent.txt --make-bed --out parent where
parent.txt consists of family ID and individual ID.
To merge parent data into 2nd population, I used:
plink --bfile file2 --bmerge parent.bed parent.bim parent.fam --make-bed --out merge
However, I noticed, after the extracting part, the number of data in .bim file still same as before. Am I using the correct commands?
Original file for population 1
wc file.* 3277 6844 4613223 file.bed 170860 1025160 5146571 file.bim 108 648 2194 file.fam
Parent file after extracting
0 1 170863 parent.bed
170860 1025160 5146571 parent.bim
1 6 19 parent.fam
Please help me. Thank you.