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mskcc / ACCESS-Pipeline

cfDNA Sequencing Pipeline with UMI
MIT License
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stricter validation for generate_access_variants_inputs #231

Open ionox0 opened 4 years ago

ionox0 commented 4 years ago

A run that has normals in the -sb folder (which is supposed to be only tumor simplex bams) errored silently and produced MAF files with no variants.

Two places this can be addressed:

  1. When creating inputs file, make sure that only the corresponding bams from the -tb bams folder are found in -sb folder (same count, with matching sample IDs)
  2. ACCESS_filters should throw an error (need to look into this more why it failed silently with zero-length MAFs)
ionox0 commented 4 years ago

Other things we should validate:


gen_var_cmo:
- check that len(pairing_file[‘tumor_id’]) == len(t)
    - ?
- check that len(t_s) == len(t_d)
- check that no normal simplex bams are genotyped… how to do this?