Nextflow workflow to postprocess StrelkaBP results annotated with VEP from Sarek.
Filters for LCR and IG regions and breaks into readable tsv file.
Based on Sareks annotation workflow
- Filter against LCR regions
- Filter against Ensembl IG regions
- Adds extra Cosmic annotation in Cosmic VCF file using snpSift
- Splits to columns with python and pandas
nextflow run postprocess.nf --outDir results --sampleID Sample_ID
Create profiles for what ANN columns to output in final file and attach name to them. E.g. CLL, minimal, maximal, custom Attach final column name with column