2012
DOI: 10.1101/gr.129684.111
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Abstract: Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of tumors. Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor-normal pairs. Unlike most current approaches, our algorithm reads data from both samples simultaneously; a heuristic and statistical algorithm detects sequence variants and classifies them by somatic stat… Show more

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Cited by 4,055 publications
(3,319 citation statements)
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References 29 publications
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“…Reads were aligned using Novoalign (http://www.novocraft.com/products/novoalign/) and further processed using Picard (http://picard,sourceforge.net/) and the Genome Analysis Tool Kit (GATK) (DePristo et al ., 2011). Somatic variants were called using VarScan2 (Koboldt et al ., 2012). …”
Section: Methodsmentioning
confidence: 99%
“…Reads were aligned using Novoalign (http://www.novocraft.com/products/novoalign/) and further processed using Picard (http://picard,sourceforge.net/) and the Genome Analysis Tool Kit (GATK) (DePristo et al ., 2011). Somatic variants were called using VarScan2 (Koboldt et al ., 2012). …”
Section: Methodsmentioning
confidence: 99%
“…SAMtools mpileup19 (0.1.19; base phred score >20 and read mapping quality >20, BAQ computation disabled), Varscan220 (v2.4.1; includes running fpfilter.pl) and MuTect21 (v1.1.7) were used to locate non‐reference positions in cell culture, tumor and germline samples. To reduce false positive variant calls, additional filtering was performed.…”
Section: Methodsmentioning
confidence: 99%
“…Applying standard settings, sequences were mapped using the alignment tool BWA (v.0.7.12) 34 . Variant calling was carried out using VarScan 2 (v.2.3.7) 35 with a minimum variant allele frequency (VAF) of 0.5% and variants were annotated using Annovar 36 . Samples from 366 patients enrolled in the UK LRF CLL4 trial were investigated by targeted NGS using a custom design TruSeq gene panel Samples with >5% VAF were considered mutated.…”
Section: Analysis Of Egr2 Mutationsmentioning
confidence: 99%