Join multiple PLINK dosage files into one file
If you have multiple PLINK dosage files and would like to merge them into one file, this script might save you some time.
A dosage file is a space-delimited table with a header. (Below, I increased spacing between the columns to increase legibility.)
Here’s an example:
SNP A1 A2 F1 I1 F2 I2 F3 I3 rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01 rs0002 G A 0.00 1.00 0.00 0.00 0.99 0.01
SNP is the name of the single nucleotide polymorphism.
A1 and A2 describe the two alleles for each SNP.
F1 and I1 correspond to the first individual. F2 and I2 to the second individual, and so on. We have three individuals in this example.
Each genotype is represented by two numbers. For individual 1, the probabilities of A/A and A/C are 0.98 and 0.02, respectively.
When dosage file 1 has SNPs that are absent from dosage file 2, we want the output file to have NA values for those SNPs in the columns corresponding to dosage file 2.