Convert phased genotype data from SHAPEIT2 format to PLINK format (plain text)

General info

Python scripts to convert phased genotype data from SHAPEIT2 format (.haps/.sample) to plain text PLINK format (.ped/.map) while keeping the phasing information intact.

1. The first step is to convert from SHAPEIT2 format (.haps/.sample) to IMPUTE2 format (.haps/.legend/.sample).
2. The second step is to convert from IMPUTE2 format (.haps/.legend/.sample) to plain text PLINK format (.ped/.map). This step uses the SHAPEIT2 .sample file from the first step and the cut command in UNIX/Linux/Mac OS X.

The script to perform the first step, convert_shapeit2_to_impute2.py, is based on a script from PyPedia. The second script, convert_impute2_to_PEDMAP.py, is written by me, because the one(s) from PyPedia (and other places) would start to use swap space for large datasets and would, therefore, become excruciatingly slow; my script avoids using swap and performs the conversion in memory for any number of individuals.

Usage

Data has to be separated by chromosome; then, run a for ((i = 1; i <= 22; i++)); do ...; done loop and perform the following steps in the loop.

1. python convert_shapeit2_to_impute2.py chr${i}.haps chr${i}.sample temp${i}.haps temp${i}.legend temp${i}.sample
2. python convert_impute2_to_PEDMAP.py temp${i}.haps temp${i}.legend chr${i}.sample chr${i} ${i}
3. rm temp${i}.*

You can comment out the third step if you would like to keep the output in IMPUTE2 format as well.

NOTE

You might need to edit convert_impute2_to_PEDMAP.py to make it consistent with your phased SHAPEIT2 .sample file in terms of the number of columns.