All somatic

All PASS-filtered calls by the NYGC pipeline

Low confidence

All somatic calls that were only called by one caller

High confidence

• SNVs/Indels: All somatic calls that were either called by two or more callers, or called by one caller and validated by Lancet or Manta SV calls

• SVs: All somatic called by two or more callers, or called by one caller with either additional support from nearby CNV changepoints or split-read support from SplazerS

CancerGeneCensus (CGC)

High confidence variants that overlap genes listed in the Tier 1 Cancer Gene Census list from COSMIC. In B-Allele Frequency plots CGC gene variants with AF >= 1% in 1000G or gnomAD are excluded

* NOTE: Lancet is only run on exonic regions, and also in validation mode to confirm variants called by 1 caller

SV: High confidence SV calls

CNV: Amplification: log2 > 0.2, Deletion: log2 < -0.235

BAF: B-Allele Frequency is the allele frequency of germline, heterozygous SNVs in the tumor sample

VAF: Variant allele frequency of High confidence SNVs

Intermutation distance: Distance between High confidence SNVs