WesPipe/README.md

# WES analysis

Automated integrated analysis software for genomics data of the cancer patients.

## Quality control
FastQC, FastQ Screen, Qualimap

## Variant calling
- SNV/Indel: TNseq (somatic), Haplotyper (germline)
- CNV: CNVkit
- SV: Manta
- TMB: in-house code
- HRD: sequenza
- MSI: MSIsensor