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Run single variant meta-analysis without aggregation tests #24

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welchr opened this issue Mar 16, 2020 · 1 comment
Open

Run single variant meta-analysis without aggregation tests #24

welchr opened this issue Mar 16, 2020 · 1 comment
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type: enhancement
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4.16.0

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@welchr
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welchr commented Mar 16, 2020

Single variant meta-analysis fails with an error unless a set test option is listed in the command, but runs fine as long as one set test flag is included. However, the command as a whole still errors out because it can’t run the set test without additional inputs. Seems there should be a way to run single variant meta-analysis without unused flags or getting command errors. This is especially a problem when running lots of jobs. They all return “error” codes in slurm, so it isn’t easy to differentiate which jobs actually worked and which ones actually failed.
welchr added a commit that referenced this issue Apr 19, 2020
@welchr
Allow skipping burden tests
0270608 
Logic was incorrect in that if no burden tests were requested, it would
still ask for a covariance matrix anyway

Fixes #24
@welchr welchr added this to the 4.16.0 milestone Apr 19, 2020
@welchr welchr mentioned this issue May 14, 2020
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@alisonrocco
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Is there any update on this issue? I've encountered the same problem:

FATAL ERROR -
Covariance files are essential to do gene-level tests. Pleaes ues --covFiles your.list.of.cov.files option.

version is 4.15.1

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@welchr @alisonrocco