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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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	This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.	Illumina HiSeq 2000	4

Publications	Citations
A comparative analysis of algorithms for somatic SNV detection in cancer. Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL. Bioinformatics 29: 2013 2223-2230	60