Improving bioinformatic pipelines for exome variant calling
نویسندگان
چکیده
منابع مشابه
Systematic comparison of variant calling pipelines using gold standard personal exome variants
The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-co...
متن کاملComparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines
Summary: To evaluate and compare the performance of variant calling methods and their confidence scores, comparisons between a test call set and a “gold standard” need to be carried out. Unfortunately, these comparisons are not straightforward with the current Variant Call Files (VCF), which are the standard output of most variant calling algorithms for high-throughput sequencing data. Comparis...
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The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scient...
متن کاملDetailed comparison of two popular variant calling packages for exome and targeted exon studies
The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we com...
متن کاملConsensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes
MOTIVATION The development of cost-effective next-generation sequencing methods has spurred the development of high-throughput bioinformatics tools for detection of sequence variation. With many disparate variant-calling algorithms available, investigators must ask, 'Which method is best for my data?' Machine learning research has shown that so-called ensemble methods that combine the output of...
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ژورنال
عنوان ژورنال: Genome Medicine
سال: 2012
ISSN: 1756-994X
DOI: 10.1186/gm306