Error when doing gwas with hail

Question

[barry_reeves]

Getting this error when doing a gwas with hail...

Error summary: ClassCastException: java.lang.String cannot be cast to java.lang.Boolean

Here is the command for the gwas...

gwas = hl.linear_regression_rows(y=mt.is_case,
                                 x=mt.GT.n_alt_alleles(),
                                 covariates=[1.0])

This is what the data looks like:

Source:
    <hail.matrixtable.MatrixTable object at 0x126ae47f0>
Index:
    ['column']
--------------------------------------------------------
--------------------------------------------------------
Type:
        struct {
        s: str,
        fam_id: str,
        pat_id: str,
        mat_id: str,
        is_female: bool,
        is_case: bool
    }

If you need more info let me know...

Thanks,

[Pierre Lindenbaum]

it's the only error message ? there is no stacktrace ?

[tpoterba]

Full stack trace would help!