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RTIInternational / biocloud_gwas_workflows

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Skip HWE filter for chrX if all male sample. #10

Closed jaamarks closed 3 years ago

jaamarks commented 3 years ago

When the sample is comprised of all males, the workflow will fail on the HWE filtering step when chrX is being processed.

Example log file on CloudWatch here.

jaamarks commented 3 years ago

We resolved this issue by creating an optional variable hwe_chrs in the main workflow that gets passed to the HWE workflow. The user can specify which chromosomes to perform the HWE wf on—i.e. whether they want to skip chrX or not.