References — Molecular pathology

Literature underpinning CTIR’s molpathR: variant analysis, NGS file-format specifications, and clinical-genomics knowledge bases.

Suggested reading

• VCF format specification — Danecek et al., 2011.
• BAM / SAMtools — Li et al., 2009.
• GATK Best Practices — Van der Auwera et al., 2013, plus current-version updates.
• ClinVar — Landrum et al., current edition.
• OncoKB — Chakravarty et al., 2017.
• AMP/ASCO/CAP variant-interpretation guidelines — Li et al., 2017.

See the disclaimer — this is a starting list, not a curated bibliography.