Entry Points Sub-workflow

Workflow File:

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

Config Options: see The config.yml for more details

  • user_files.gtc_pattern

  • user_files.idat_pattern

  • user_files.ped

  • user_files.map

  • user_files.bed

  • user_files.bim

  • user_files.fam

Major Outputs:

  • sample_level/samples.bed

  • sample_level/samples.bim

  • sample_level/samples.fam

There are three paths we can take to create these files:

  1. If GTC files are provided using user_files.gtc_pattern then we will

../_images/entry-points_gtc.png

Fig. 2 The GTC entry-point workflow. If per sample GTC files are provided, then we will convert these files to the PED/MAP format and merge them together.

  1. If an aggregated PED/MAP is provided using user_files.ped and user_files.map then we will convert the PED/MAP to BED/BIM/FAM.

  2. If an aggregated BED/BIM/FAM is provided using user_files.bed, user_files.bim, user_files.fam then we will create a symbolic link.