Question: Error when doing gwas with hail
0
gravatar for barry_reeves
5 weeks ago by
barry_reeves0 wrote:

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,

hail gwas • 113 views
ADD COMMENTlink modified 26 days ago by Biostar ♦♦ 20 • written 5 weeks ago by barry_reeves0

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

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum119k

Full stack trace would help!

ADD REPLYlink written 25 days ago by tpoterba40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1687 users visited in the last hour