clinical-filtering

Repository for clinical filtering for SNV/Indels and/or SVs.

Each v0.x is associated with a published Dockstore workflow.

filterClinicalVariantsSNVIndel_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-variants-SNV-Indel-v01

• SNV/Indel clinical filtering.

filterClinicalVariantsSV_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-variants-SV-v01

• SV clinical filtering.

filterClinicalCompHets_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-comphets-xlr-hom-var-v01

• Outputs comphets, XLR, and homvar in proband from SNV/Indel and/or SV input.

filterClinicalVariants_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-variants-v01

• Combines filterClinicalVariantsSNVIndel_v0.1.wdl,filterClinicalVariantsSV_v0.1.wdl, and filterClinicalCompHets_v0.1.wdl into one workflow.

filterClinicalVariantsNIFS_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-variants-NIFS-v01

• SNV/Indel only. Run at sample-set level.
• Combines filterClinicalVariants_v0.1.wdl and filterClinicalCompHets_v0.1.wdl into one workflow, with some differences in filters.

filterClinicalVariantsSingleNIFS_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/filter-clinical-variants-single-NIFS-v01

• SNV/Indel only. Run at sample level.

mergeClinicalVariantsNIFS_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/clinical-filtering/merge-clinical-variants-NIFS-v01

• Merge runs of filterClinicalVariantsSingleNIFS_v0.1.wdl (so that when new samples need to be run, not all samples have to be rerun).

Utility Scripts

This folder contains scripts for basic clinical data procesing parseGeneMap2_Step1.py: Parses a genemap file parseGeneMap2_Step2.py: Parses a output from step 1 into a file with: gene name, inheritance code

TODO: Generally want to add scripts to the Docker images for each task/workflow instead of having them as WDL inputs, but not a priority.