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A Comparative Analysis of Algorithms for Somatic SNV Detection in Cancer

Four recently published algorithms for the detection of somatic SNV sites in matched cancer-normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer- normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterised and compared to investigate the strengths and weaknesses of each SNV calling algorithm.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001000967 Illumina HiSeq 2000 4
Publications Citations
A comparative analysis of algorithms for somatic SNV detection in cancer.
Bioinformatics 29: 2013 2223-2230