• Supplemental Video 1. Animated primary versus relapse SciClone plots at various sequencing depths (.gif format | .mp4 format).
• Supplemental Dataset 1. 371,976 somatic variants called by seven different variant callers run on the WGS data. This list includes readcounts from WGS and a listing of which callers detected each site. The file is hosted on dbGaP, since some variants were ultimately determined to be germline (dbGaP accession phs000159). A detailed description of the columns in this TSV file is provided here: Supplemental_Dataset_1-AllSomaticSnvCalls.Definitions.xlsx.
• Supplemental Dataset 2. 198,814 variants validated on a Nimblegen custom capture array. This list includes readcounts from all sequence datasets and RNAseq. The file is hosted on dbGaP, since some variants were ultimately determined to be germline. (dbGaP accession phs000159). A detailed description of the columns in this TSV file is provided here: Supplemental_Dataset_2-SomaticSnvsTargetedForValidation-ReadCounts.Definitions.xlsx.
• Supplemental Dataset 3. "Platinum" list of 1,343 validated somatic SNVs. These are highly-confident variant calls derived from ultra-deep sequencing, extensive filtering, and manual curation. This list includes readcounts from all sequence datasets and RNAseq, along with clonal cluster assignments. Full details can be found in the Supplemental Methods.
• Supplemental Dataset 4. "Gold" list of 3,959 somatic SNVs. This list contains all the platinum sites, plus an additional 2,615 sites that are potentially valid, but did not meet the threshold of evidence that we required for the platinum list. In most cases, deeper sequencing would be needed to verify these SNVs. Full details can be found in the Supplemental Information.
• Caller Performance, using the platinum list as a truth set. For a full description of the parameters used for each caller, see the Supplemental Methods. Key below:
  • uni = union of two or more callers
  • int = intersection of two or more callers
  • bas = Bassovac
  • mut = Mutect
  • seu = Seurat
  • shi = Shimmer
  • sni = Sniper
  • str = Strelka
  • var = VarScan