arontommi / SarekCLLPostProcess

Process StrelkaBP results from Sarek

Sarek CLL Postprocess

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

Steps

1. Filter against LCR regions
2. Filter against Ensembl IG regions
3. Adds extra Cosmic annotation in Cosmic VCF file using snpSift
4. Splits to columns with python and pandas

Usage

nextflow run postprocess.nf --outDir results --sampleID Sample_ID

ToDo

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