ArticleCurrent protocols in bioinformatics2013
Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection.
Article in Current protocols in bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
- Trial
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- The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.PLoS genetics · 2016Trial
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- Systematic evaluation of de novo mutation calling tools using whole genome sequencing data.Briefings in bioinformatics · 2025Article
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- Non-truncating BMPR1A variants associated with familial colorectal cancer and adenomatous polyps.BMC cancer · 2025Article
- C to U RNA editing of MFN1 is regulated by ADARB1 and associates with favourable prognosis in chronic lymphocytic leukemia.Scientific reports · 2025Article
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- M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications.GigaScience · 2025Article
86 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
The identification of small sequence variants remains a challenging but critical step in the analysis of next-generation sequencing data. Our variant calling tool, VarScan 2, employs heuristic and statistic thresholds based on user-defined criteria to call variants using SAMtools mpileup data as input. Here, we provide guidelines for generating that input, and describe protocols for using VarScan 2 to (1) identify germline variants in individual samples; (2) call somatic mutations, copy number alterations, and LOH events in tumor-normal pairs; and (3) identify germline variants, de novo mutations, and Mendelian inheritance errors in family trios. Further, we describe a strategy for variant filtering that removes likely false positives associated with common sequencing- and alignment-related artifacts.
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