Intensity check Sub-workflowΒΆ

Workflow File:

https://github.com/NCI-CGR/GwasQcPipeline/blob/default/src/cgr_gwas_qc/workflow/sub_workflows/intensity_check.smk

Config Options: see The config.yml for more details

  • user_files.bcf or user_files.idat_pattern

Major Outputs:

  • sample_level/contamination/median_idat_intensity.csv aggregated table of median IDAT intensities.

bcf_input_intensity idat_input_intensity

The Intensity check sub-workflow. This workflow will calculate the median intensity for each sample individually. It requires that you have an aggregated BCF or IDAT files.