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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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Allow user to set a gnomad allele freq threshold for filtering #112

Closed malachig closed 1 year ago

malachig commented 1 year ago

maximum_population_allele_frequency is used to filter variants with GNOMAD allele frequency > than this value. The default is set in detect_variants to 0.001. If a variant has gnomad_field_name > this value, it gets filtered out.

https://github.com/wustl-oncology/analysis-wdls/blob/16eb3925223ca4bd47f6a5282c219fa981d187eb/definitions/detect_variants.wdl#L65

https://github.com/wustl-oncology/analysis-wdls/blob/16eb3925223ca4bd47f6a5282c219fa981d187eb/definitions/subworkflows/filter_vcf.wdl#L16

https://github.com/wustl-oncology/analysis-wdls/blob/16eb3925223ca4bd47f6a5282c219fa981d187eb/definitions/tools/filter_vcf_custom_allele_freq.wdl#L6

BUT, this parameter is not exposed up to the pipelines. We would like to be able to set this in immuno.wdl.

One use case would be to essentially turn off GNOMAD filtering by setting: immuno.maximum_population_allele_frequency: 1.

malachig commented 1 year ago

Closing this issue which has now been resolved by the PR above.