Recode Filtering Scripts into a python package.

[rhshah]

It should include the following:

• filter_variants (this should filter the file)
  • filter_vardict: https://github.com/mskcc/ACCESS-Pipeline/blob/master/cwl_tools/basicfiltering/filter_vardict.py
  • filter_mutect: https://github.com/mskcc/ACCESS-Pipeline/blob/master/cwl_tools/basicfiltering/filter_mutect.py
  • filter_by_annotation :https://github.com/andurill/ACCESS-Pipeline/blob/master/cwl_tools/remove_variants_by_anno/remove_variants_by_annotation.py (move to tags instead of remove)
• tag_variants (this should add tags in FILTER column of MAF)
  • hotspots: https://github.com/mskcc/ACCESS-Pipeline/blob/master/cwl_tools/hotspots/tag_hotspots.py
  • germline: https://github.com/mskcc/ACCESS-Pipeline/blob/master/python_tools/workflow_tools/ACCESS_filters.py#L244
  • below_threshold: https://github.com/mskcc/ACCESS-Pipeline/blob/master/python_tools/workflow_tools/ACCESS_filters.py#L253
  • occurence_in_curated_normals: https://github.com/mskcc/ACCESS-Pipeline/blob/master/python_tools/workflow_tools/ACCESS_filters.py#L262
  • occurence_in_normal: https://github.com/mskcc/ACCESS-Pipeline/blob/master/python_tools/workflow_tools/ACCESS_filters.py#L267
  • blacklist: https://github.com/mskcc/ACCESS-Pipeline/blob/master/python_tools/workflow_tools/ACCESS_filters.py#L280

[rhshah]

@ionox0 @andurill @maysunh please let me know your thoughts on reorganizing this code. Please do let me know if I am missing parts of the variant calling process, by looking here: https://github.com/orgs/msk-access/projects/2