Checking if lead variants are novel or not

GWASLab can check if the lead variants of your summary statistics overlap with reported variants or not based on the physical distance.

.get_novel()

sumstats.get_novel(
                    known,
                    efo,
                    only_novel=False,
                    windowsizekb_for_novel=1000,
                    windowsizekb=500,
                    sig_level=5e-8,
                    output_known=False)

GWASLab checks overlap with a local file of variants or records in GWASCatalog.

Required (either):

• known : string, path to the local file of reported variants

or

• efo : string, EFO id for the target trait, which is used for querying the GWASCatalog.

Options

.get_lead() options	DataType	Description	Default
windowsizekb	int	Specify the sliding window size in kb	500
sig_level	float	Specify the P value threshold	5e-8
windowsizekb_for_novel	int	windowsize for determining if lead variants overlap with reported variants in GWASCatalog	1000
only_novel	boolean	output only novel variants	False
output_known	boolean	additionally output the reported variants	False
verbose	boolean	If True, print logs	True

EFO ID

You can find the efo id by simply searching in GWASCatalog. For example, the EFO ID for T2D can be obtained :

Example

Only works when your sumstats are based on GRCh38

Only associations with the EFO trait will be obtained. This does not include associations with child traits.

Example

See Lead and novel variants

Reference

• Buniello, A., MacArthur, J. A. L., Cerezo, M., Harris, L. W., Hayhurst, J., Malangone, C., ... & Parkinson, H. (2019). The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic acids research, 47(D1), D1005-D1012.