Included chrX VCF fails due to containing NA in FILTER column.
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aofarrel commented
When WDLizing this pipeline, I found this issue. When I replicated it in both the CWL version and the raw R scripts, I realized it's not related to WDL. If we filter the VCF to remove all rows that contain NA for FILTER, then check_gds will complete successfully.
aofarrel commented
Link to a filtered chrX that I've been using for testing since: https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/testdata/1KG_phase3_subset_chrX.vcf
This filtered chr passes on the CWL and WDL version of this pipeline, and should pass the original pipeline here too.
smgogarten commented