dkfz-odcf/snvcallingworkflow

The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow

snvcallingworkflow's Issues

Add VEP annotations to the somatic SNVs

Feature Requirements:

• Add VEP annotations to the SNV calls.
• Parse transcripts with "HIGH" or "MODERATE" VEP consequences impact from the INFO column and add them to a new column with Gene, Consequences, Exon/Intron counts, HGVSc and HGVSp information.
• Still to be decided:
  • Should this be done for all variants?
  • Should the VEP annotation be removed from the INFO column once it is parsed?

Make output MultiQC compatible

MultiQC simplifies the visual representation of QC data. For display in MultiQC result files either should be one of the already supported formats or can be annotated. Check the output files and restructure their content to support MultiQC.