README.md

synoptiko

Summary report of somatic mutations from cancer DNA sequencing data

Usage

synoptiko --vcf mutect.vcf --vcf mutect2.vcf
                total variants:   680
                        # SNVs:   630
                      # indels:    50
coding non-synonymous variants:   150
===

Coding variants in known cancer genes:
-- LATS2 p.R352L (chr13 g.21562864C>A)
-- FLT3 p.R387L (chr13 g.28622457C>A)
-- TP53 p.C141Y (chr17 g.7578508C>T)
-- DNMT3A p.R484W (chr2 g.25468913G>A)
-- NFE2L2 p.LWRQDIDLGVSREVFDFSQ22del (chr2 g.178098921_178098977delGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAA)
-- ZNF133 p.Q533K (chr20 g.18297095C>A)

Coding variants in MHC-I presentation genes:
-- HLA-C p.R155G (chr6 g.31239006G>C)

Coding variants in interferon response genes:
    none