If you have multiple PLINK dosage files and would like to merge them into one file, this script might save you some time.

Dosage files#

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.

Source code#

Download join_dosage_files.py