Depth for T/N WGS

[PMID:26647970] [Nature Communications]

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

“Recommended checklist for WGS cancer studies:

  • PCR-free library preparation
  • Tumour coverage >100 ×
  • Control coverage close to tumour coverage (±10%)
  • Reference genome hs37d5 (with decoy sequences) or GRCh38 (untested)
  • Optimize aligner/variant caller combination
  • Combine several mutation callers
  • Allow mutations in or near repeats (regions of the genome likely to be more prone to mutation)
  • Filter by mapping quality, strand bias, positional bias, presence of soft-clipping to minimize mapping artefacts”
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