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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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125 fix germline variant calling #128

Closed evelyn-schmidt closed 11 months ago

evelyn-schmidt commented 1 year ago

This PR is related to issue #125

Enables the user to override the default for filtering of germline SNPs

evelyn-schmidt commented 1 year ago

The change has been tested with germline_filter_gnomAD_maximum_population_allele_frequency set at three separate values: 1.1 (which results in no filtering), .05, and .01 (which results in extreme filtering).

To verify that these changes took place, I viewed the intermediate files between the gnomadFrequencyFilter step and the setFilteredVcfName (within germline_filter_vcf.wdl). After investigating these files I found that the run with the filter of 1.1 resulted in files that were the exact same size with the same values (as expected) while the run with the filter of 0.01 had a file that was significantly smaller in size than the pre-filtering file, removing all entries with a gnomAD AF above 0.01.

Users can now set the value within the yaml file or choose not to set it, in which the default value will be 1.1 resulting in no filtering.

evelyn-schmidt commented 1 year ago

Looks like a few files in this PR ended up with mode changes.

Those files have now been fixed.