Liftover

GWASLab can directly liftover the positions of variants in sumstats.

.liftover()

mysumstats.liftover(n_cores=3, 
                    from_build="19", 
                    to_build="38",
                    remove=True)

Note

GWASLab will only liftover basepair positions. If needed, please perform harmonization using the reference file of the target build.

Options

.liftover() options	DataType	Description	Default
n_cores	int	Number of threads to use for liftover.	1
from_build	"19" or "38"	Original genome build	-
to_build	"19" or "38"	Target genome build	-
remove	boolean	If True, remove unmapped variants	True

Quote

This method is based on GitHub - jeremymcrae/liftover: liftover for python, made fast with cython

Example

Example

mysumstats.liftover(n_cores=3, from_build="19", to_build="38")