High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions. Additional computational techniques have proved useful for defining the mutations, genes and molecular networks that drive diverse cancer phenotypes and that determine clonal architectures in tumour samples. Collectively, these tools have advanced the study of genomic, transcriptomic and epigenomic alterations in cancer, and their association to clinical properties. Here, we review cancer genomics software and the insights that have been gained from their application.
At a glance
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The GATK is a broad and widely used toolkit for variant discovery and data processing.
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VarScan (described in references 24 and 25) is one of the early programs for somatic SNV detection and has since added additional capability for germline, copy-number and indel events.
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SAMtools is a broad set of utilities for processing sequence data in the standardized SAM/BAM format, including variant calling.
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Pindel is focused on identifying breakpoints at single-base-resolution of indels, inversions and tandem duplications.
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