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pmbcl_exomes's Introduction

Primary Mediastinal B-Cell Lymphoma (PMBCL) exomes

Study design

  • 95 tumor samples
  • 21 matching normals
  • Whole exome sequencing performed on all samples (average 115X)

Variant calling

Tumor samples with a matching normal were analyzed using a paired analysis. For unpaired samples, tumors were matched against a pooled normal (10 of the 21 normals downsampled and merged). The following callers were applied to determine somatic nucleotide variants and indels:

  • VarScan
  • MuTect
  • Strelka
  • MutSig to identify significantly mutated genes

Copy number detection

  • CNVkit
  • GISTIC to identify signficant amplications and deletions

pmbcl_exomes's People

Contributors

stacyhung avatar

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